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Bookkeeping Software for Business: How to Choose What’s Right for You

Bookkeeping Software for Business: How to Choose What’s Right for You

Written by 
Pilot Team
June 21, 2019
Bookkeeping Software for Business: How to Choose What’s Right for You

If you’re looking for the right bookkeeping software for your business, it’s impossible to miss how many different tools there are on the market. Some are geared more towards freelancers, while others provide the most value for entire accounting departments.

How do you know which one is right for you or your organization? In this post, we’ll dive into some commonly asked questions then list 25 popular bookkeeping software options, along with who they’re best for.

Here’s what we cover:

Read the whole thing for a more complete understanding of the topic, or skip to the sections that interest you most.

Note: At Pilot, we have a team of expert bookkeepers (with software superpowers). Let us take the bookkeeping burden off your plate: Try Pilot Now.

What’s the Difference Between a Bookkeeper and Bookkeeping Software?

Bookkeeping is the act of managing and recording the financial aspects of your company. Bookkeeping software helps a business owner or bookkeeper manage that data. Here’s a more in-depth explanation:

A bookkeeper is the person who is tasked with this job, and while their actual duties can vary from client to client, here are four general services that they can perform:

  • Categorize transactions from PayPal, credit cards, payment processors, etc., and ensure that they’re accounted for in company books.
  • Prepare key financial statements such as profit and loss, balance sheets, and the statement of cash flow report.
  • Reconcile your bank statements with transaction records.
  • Manage the accounts receivable and accounts payable of a business.

A good bookkeeper is someone who is both experienced and passionate about helping you grow your business. They should have the ability to take complicated financial terms and concepts and break them down into easy-to-understand language. Most importantly, your bookkeeper should provide insightful financial data, which you can use to make intelligent business decisions as well as scale and grow your business.

Bookkeeping software helps you or your bookkeeper manage a wide variety of bookkeeping functions, such as creating reports, record keeping, and balancing the books, to name a few.

For example, many bookkeeping software tools can connect seamlessly with your bank account to import transactions and other financial data. This not only helps save time over entering transactions manually, but it also reduces the human error element that comes with manual data entry.

What Are the Differences Between Bookkeeping Software and Accounting Software?

There are very few differences, if any, between bookkeeping and accounting software. They usually have the functionality to perform both bookkeeping and accounting tasks. The main difference is in how the software is used by accountants vs. bookkeepers. To understand that, you have to understand how their roles are different.

Bookkeepers perform a wide range of duties, such as recording financial transactions, maintaining accurate records, and balancing the books of a business. They also can prepare key financial statements and help translate them into plain English so business owners can use that information to make intelligent business decisions.

A bookkeeper is someone who manages the financial information of a business. They’re not technically qualified to give financial advice or perform strategic planning. There are no licensing requirements, and anyone can become one.

An accountant, on the other hand, is someone who is certified to perform accountant-related duties that can include strategic planning, tax preparation, and creating financial reports. Accountants are required to have a Bachelor’s degree in business or another related field. They must then pass a comprehensive exam to receive their Certified Public Accountant (CPA) license.

In short, bookkeepers will manage and record the financial information of a business, while accountants can interpret it, provide qualified advice, and prepare taxes.

Bookkeeping software allows bookkeepers and accountants alike to handle tasks and functions such as:

  • Accounts payable
  • Accounts receivable
  • Categorizing transactions
  • Financial close management
  • General ledger
  • Preparing key financial statements
  • Purchase orders and stock/inventory
  • Reconciling bank accounts.

Should I Use Paid or Free Bookkeeping Software?

Generally speaking, paid software offers more functionality than free software. However, that’s not to say free bookkeeping software isn’t useful for certain types of businesses.

For example, companies like Wave offer free accounting, invoicing, and receipt scanning software. But these kinds of free software tools are only sensible for very small companies and one-man bands. Most companies would do better on software that provides more features and tooling, plus a greater ability to scale as the business grows.

How Do You Choose the Bookkeeping Software Best for Your Business?

You can choose the right bookkeeping software by first looking at the challenges that your business needs to solve.

For example, a freelancer might find more value in a bookkeeping tool that provides just a few basics, like invoicing and credit card processing. An enterprise-level company would benefit from software that offers an extensive set of powerful accounting tools that accommodates many users. Startups are usually better off with software that has the potential to keep pace as they rapidly scale in size.

To help businesses of every size, we’ve compiled 25+ popular bookkeeping software tools currently on the market:

QuickBooks Online (Our Top Choice)

Bookkeeping Software: QuickBooks Online
  • Pricing: 30-day free trial. Pricing starts at $20/month (after promo period ends). The Plus plan is $70/month (after promo period ends).
  • Rating: 4.0/5 on G2Crowd.
  • Who it’s for: Small, medium, large, and early enterprise-level businesses. QuickBooks is especially great for startups since it can scale with their growth.

QuickBooks Online is one of the most popular bookkeeping software tools on the market. It’s used by millions of organizations, bookkeepers, and accountants to manage the finances of companies of all sizes.

Some of the best things about QuickBooks Online are its versatility and the wide range of important functions it performs. It helps keep records and organize expenses, taxes, and sales.

It scales as your business grows and is the ideal choice if you need your software to handle increasingly complex situations and manage an increasing number of transactions. (You might run into a transactional cap with many other tools on the market.)

All of this information is viewable on a customizable dashboard or through one of many different accounting or bookkeeping reports. Freelancers and businesses without an internal accounting department can easily invite their CPA to connect and download their information for end-of-year tax purposes.

Best of all, QuickBooks Online integrates seamlessly with a wide variety of platforms and apps such as PayPal, Square, and American Express.

Note: Because it’s so versatile and scalable, our bookkeepers do all our clients’ bookkeeping in QuickBooks Online. If you’d like to hand off bookkeeping and free up your time, Try Pilot Now.


Bookkeeping Software: Xero
  • Pricing: The starter plan is $20/month. Premium is $40/month.
  • Rating: 4.2/5 on G2Crowd.
  • Who it’s for: Small businesses that need an all-in-one online accounting software solution.

Xero is a cloud accounting software solution for small businesses. In addition to the usual features that come with an all-in-one online accounting solution, it also has a robust payment management and collection tool and can perform double-entry accounting.

It also allows businesses to add online payment options to invoices—accepting payments through PayPal, Apple Pay, or Stripe—and then it logs those transactions in the system.


Bookkeeping Software: Wave
  • Pricing: Accounting, invoicing, and receipt scanning functionality are free. See site for individual payment accepting and payroll service plans.
  • Rating: 4.4/5 on G2Crowd.
  • Who it’s for: Small businesses who need free accounting software that performs basic accounting, expense tracking, invoicing, receipt software. Also has credit card accepting and payroll functionalities.

Wave offers free accounting, invoicing, and receipts software that helps freelancers and small business owners run their businesses more efficiently. It also has credit card processing and payroll features that are both paid. There’s even a mobile app that can accept payments on the go.

Businesses can also link their PayPal and bank accounts to the software to generate tax records, balance sheets, and accounts receivable/payable reports. Wave is a great way for small businesses to manage their accounting and bookkeeping without getting bogged down with complicated features they may not need.

Note: Are you unsure as to whether Xero or Wave is right for your business? Check out our QuickBooks vs. Xero vs. Wave comparison post for a more in-depth look at all three tools.


Bookkeeping Software: FreshBooks
  • Pricing: 30-day free trial. Plans start at $15/month for up to 5 clients. Contact for enterprise pricing.
  • Rating: 4.6/5 on G2Crowd.
  • Who it’s for: Solopreneurs, self-employed, small businesses.

FreshBooks allows you to track time and expenses, plus send professional-looking invoices to clients. Many freelancers and small businesses love it because it simplifies the often time-consuming aspect of accounts receivable.

FreshBooks also offers your clients the option of paying their invoices via credit or debit card. The processing fees are on par with other online payment accepting gateways. It’s an excellent choice for businesses that don’t need a fully-fledged accounting application or invoicing software.


Bookkeeping Software: NetSuite
  • Pricing: Contact for pricing.
  • Rating: 3.9/5 on G2Crowd.
  • Who it’s for: Enterprise-level companies.

NetSuite is a cloud Enterprise Resource Planning (ERP) system designed to help the accounting departments of businesses run more fluidly. It does this by providing a robust set of features and functionalities that can alleviate time spent on mundane tasks (such as inventory tracking and management).

From accounts payable to receivable, it offers a highly customizable platform that will wrap around the way you do business.

NetSuite also provides what they call a SuiteSuccess team. This team of experts provides customer support, technical advice on how to resolve setup issues, and “best practices” tips for new and existing users.

Many businesses will value this service, as it can help save a lot of time and get new users quickly up to speed.

Bill.com (Recommended)

Bookkeeping Software: Bill.com
  • Pricing: Plans start at $29/month. Contact for enterprise-level pricing.
  • Rating: 4.2/5 on G2Crowd.
  • Who it’s for: Any business needing accounts payable and receivable automation that connects with other platforms like QuickBooks, Sage, Xero, and Oracle.

Bill.com helps automate tedious accounts payable and accounts receivable work. It seamlessly connects with Sage Intacct, Oracle NetSuite, Xero, and QuickBooks. The Android or iOS app ensures you can stay connected even when out of the office.

Many businesses find the automated payment features useful, as Bills.com can automatically send out paper checks in the mail to contractors and vendors. It gives you full control over your AR and AP and eliminates the need for tedious manual data entry.

Bill.com also recently acquired Invoice2go in September 2021.

Sage 50cloud

Bookkeeping Software: Sage 50cloud
  • Pricing: Plans start at $46.83/month for one user. Contact for enterprise pricing.
  • Rating: 3.6/5 on G2Crowd.
  • Who it’s for: Small, medium, large, and enterprise-level companies.

Sage 50cloud is an all-in-one online accounting platform for small to medium-sized businesses. It offers features such as budgeting, cash flow, invoicing, and tax management.

It will also connect to your bank accounts so you can perform usual accounting activities such as tracking receivables, making deposits, and transferring funds. Sage 50cloud also offers a wide range of features such as payroll and credit card processing.

Expensify (Recommended)

Bookkeeping Software: Expensify
  • Pricing: 6-week free trial. Plans start at $4.99/month for individuals. Group plans start at $5 per month/per user.
  • Rating: 4.3/5 on G2Crowd.
  • Who it’s for: Small and medium sized businesses who need an efficient way to track expenses as well as manage and catalog receipts.

One of the more time-consuming aspects of managing your bookkeeping is manual data entry. Expensify extracts expense information from invoices or receipts. It then prepares and sends the data to your accounting software in just a few seconds.

You can take a photo of your receipts or invoices with your cell phone, upload via your desktop, or forward them to a dedicated and unique Receipt Stash email address. You can create your own rules, and the system will automatically categorize and add pertinent information such as tax rates or nominal codes.


Bookkeeping Software: Tipalti
  • Pricing: Contact for pricing.
  • Rating: 4.4/5 on G2Crowd.
  • Who it’s for: Large to enterprise-level companies that require accounts payable, global mass card payments, or B2B payment software.

Tipalti helps automate mass payments on a global scale. It’s designed for companies that accept a huge amount of online payments on a daily basis. Tipalti is also designed to help save time by taking over the management of accounts receivable and supplier payments.

It also has a robust fraud detection system that enables companies to flag and pinpoint potential fraud transactions before the payment is processed. Tipalti will ultimately help finance teams reduce the time they spend on payment management by automating a good portion of the busy work.


Bookkeeping Software: Goby
  • Pricing: Contact for pricing.
  • Rating: 4.6/5 on G2Crowd.
  • Who it’s for: Accounts payable automation for enterprise-level companies.

Goby automates the accounts payable process by streamlining approvals and invoice capture, and it helps eliminate the human error factor (which can contribute to excessive late fees).

It uses enhanced validation algorithms to identify trends and reveal insights—which allows for more informed budget and business decisions. Goby is a way to save time and money by automating part of the accounts payable process.

Zoho Books

Bookkeeping Software: Zoho Books
  • Pricing: Basic plan starts at $9/month. Professional plan is $29/month.
  • Rating: 4.6/5 on G2Crowd.
  • Who it’s for: Small, medium, or large businesses who need online accounting software.

Zoho Books is an online accounting solution that helps businesses track both income and expenses. It provides an easy-to-use, end-to-end accounting system that helps save time through their intelligently laid-out dashboard.

Zoho Books also offers several tax compliance features such as automatic calculations, payments, sales tax, and 1099 reporting. It also integrates with a wide range of apps such as payment gateways and point-of-sale apps.

Accounting Seed

Bookkeeping Software: Accounting Seed
  • Pricing: Contact for pricing.
  • Rating: 4.3/5 on G2Crowd.
  • Who it’s for: Enterprise-level companies who need online accounting software to help manage their business finances.

Accounting Seed is an ERP and accounting platform designed primarily for enterprise-level companies. It also offers a dashboard that provides real-time insights into the current financials of the company.

Accounting Seed natively integrates with Salesforce and they claim it is flexible enough to handle the accounting needs for large companies in any niche or industry. It allows users to create highly customizable processes that work best for the way the company does business.


Bookkeeping Software: SBS
  • Pricing: Plans start at $46.83/month for one user. Contact for enterprise pricing.
  • Rating: 3.6/5 on G2Crowd.
  • Who it’s for: Companies who need core financials, payroll, purchasing, and HR software.

SBS, Software Business Systems, is an integrated suite of software services that offers payroll, core financials, and even HR management software. It’s also great for managing projects from an expense and time standpoint.

SBS integrates fully with QuickBooks for easy exportation of data. This seamless integration helps prevent costly data entry issues that sometimes come with manual data entry.

Patriot Accounting

Bookkeeping Software: Patriot Accounting
  • Pricing: 30-day free trial. $15/month for online accounting and $10/month for basic online payroll.
  • Rating: 4.8/5 on G2Crowd.
  • Who it’s for: Small, medium, and large companies who need payroll and accounting software.

Patriot offers both payroll and accounting software designed to make life easier for small, medium, or large companies.

The robust and easy-to-use dashboard helps perform a wide variety of general accounting tasks, such as paying vendors, invoicing, and recording financials.

The payroll functionality is also user-friendly and offers basic and full-service payroll options. Users can also add HR and Time & Attendance software as add-ons to the full-service option.


Bookkeeping Software: Multiview
  • Pricing: Contact for pricing.
  • Rating: 4.5/5 on G2Crowd.
  • Who it’s for: Small, medium, large, and enterprise-level companies that require ERP and general accounting software.

Multiview is a Cloud ERP accounting system that is designed to scale alongside your business as it grows. In addition to the standard ERP offerings, it also offers a powerful dashboard and reporting system that shows company financials at a glance.

Multiview comes with a budgeting and forecasting feature, which allows users to create budget approval workflows and then compare those to actual results.


Bookkeeping Software: Divvy
  • Pricing: Free
  • Rating: 3.6/5 on G2Crowd.
  • Who it’s for: Companies that need automated expense reporting and online payment reminders.

Some companies require automated expense reporting and online payments — Divvy is great for both. Once set up, the entire process is completely automated and helps companies manage online subscriptions and eliminate wasteful spending.

Users can generate expense reports to see who’s spending what and where. This can help alleviate the stress of someone overspending on their expense account before the end of the month.


Bookkeeping Software: Canopy

  • Pricing: See website for multiple pricing levels that are based on which features you choose.
  • Rating: 3.5/5 on G2Crowd.
  • Who it’s for: Tax firms that need tax software.

Canopy is primarily designed for tax firms and helps automate menial and other time-consuming tasks so CPA’s can focus on more important work during tax time. It also comes with several features that help provide a more connected and transparent client experience.

Canopy comes with a fully featured client portal that allows for online payments, secure transmission of documents, and communication. It can help cut down on time wasting and unnecessary client phone calls when tax season rolls around.

Plus & Minus

Bookkeeping Software: Plus & Minus Software Corp.
  • Pricing: $1,000 per user.
  • Who it’s for: Businesses who require fully featured accounting/ERP software.

Plus & Minus is for businesses of all sizes who need a full-service accounting and/or ERP platform. It comes with six main functionalities: AP, AR, payroll, inventory management, cash management, and general ledger.

Other functionalities include job cost, foreign and multi currency, and email management, to name just a few.


Bookkeeping Software: OneUp
  • Pricing: 30-day free trial. Plans start at $9/month for one user. Unlimited plan is $169/month.
  • Rating: 4.3/5 on G2Crowd.
  • Who it’s for: Small businesses needing accounting and bookkeeping automation.

Small businesses will appreciate the automated features of OneUp. It connects directly to bank accounts and performs many accounting tasks automatically. To get started, simply add your bank feeds, categorize your expenses, and over the course of a few days, OneUp will learn your behavior and start to categorize automatically.

At the end of the year, your accountant can log into the software and instantly export the data to an accounting system of their choosing.

Anytime Collect

Bookkeeping Software: Anytime Collect
  • Pricing: Plans start at $46.83/month for one user. Contact for enterprise pricing.
  • Rating: 3.6/5 on G2Crowd.
  • Who it’s for: Small, medium, and large companies who need comprehensive AR management software.

Anytime Collect performs automated accounts receivable credit and collections. It’s designed primarily for businesses who sell on credit terms.

It can automate cash forecasting, invoice presentment, dispute management, and online bill pay, to name just a few of its functions.

Anytime Collect can help cut down on bad debt by automating a good portion of the AR busywork that ties up the finance department.


Bookkeeping Software: Accurants
  • Pricing: Free for one user. Paid plans start at $25/month. Call for enterprise pricing.
  • Rating: 3.9/5 on G2Crowd.
  • Who it’s for: Small businesses that need a complete all-in-one accounting system that includes CRM, bank reconciliation, invoicing, time & expense, and tax preparation.

Accurants helps businesses get paid faster and more efficiently through their complete small business management system. It’s thoroughly thought out and addresses many of the day-to-day needs of sole proprietors and freelancers.

In addition to the accounting module, it also comes with invoicing, project management, CRM, time/expense, and tax preparation functionalities that can eliminate the need for a huge software stack.

GoDaddy Bookkeeping

Bookkeeping Software: GoDaddy Bookkeeping
  • Pricing: Plans start at $4.99/month for one user. Premium is $14.99/month.
  • Rating: 4.0/5 on G2Crowd.
  • Who it’s for: Small businesses who need a suite of software services such as bookkeeping, invoicing, and importation of online sales data.

GoDaddy Bookkeeping is an automated bookkeeping system designed to save both time and money. While it may not have the robust functionality of other bookkeeping software, it does perform very well on a basic level.

This software is excellent for those who don’t need all the bells and whistles of more expensive and complicated bookkeeping software. GoDaddy Bookkeeping will walk you through the entire process and is perfect for those who don’t know a lot about finances.


Bookkeeping Software: Kashoo
  • Pricing: 14-day free trial. Plans start at $199/year.
  • Rating: 4.9/5 on G2Crowd.
  • Who it’s for: Easy-to-use accounting software for small businesses.

Kashoo is another great tool for small business owners who don’t need complex or confusing features and functionality in their accounting software. Users can quickly send invoices, accept online and offline payments, and generate informative financial management reports with a few clicks of the mouse.

Kashoo is beneficial for those who don’t have a lot of accounting experience. The dashboard is laid out intuitively and provides plenty of helpful hints and tips so users won’t feel overwhelmed (as they might with other accounting software).


Bookkeeping Software: AccountEdge
  • Pricing: 30-day free trial. Basic software is $149. Pro software is $399.
  • Rating: 4.0/5 on G2Crowd.
  • Who it’s for: Small business accounting software with cloud accounting and ERP solutions.

AccountEdge is a bit unique when compared to other full-featured accounting software

platforms. It’s a stand-alone desktop program that resides on your computer instead of the cloud.

This adds an extra layer of security, as everything is done locally, and you’re not transmitting personal information over the internet as you would with a cloud solution.

There’s a one-time fee of either $149 or $399, and no monthly subscriptions. In addition to the accounting features, users can also accept credit cards, bill for time, track inventory, and administer payroll.


Bookkeeping Software: MineralTree
  • Pricing: Contact for pricing.
  • Rating: 4.3/5 on G2Crowd.
  • Who it’s for: Companies with a large number of payments each month who want accounts payable automation.

MineralTree is designed for accounts payable and payment automation. It’s made for companies who make 500-10,000+ payments per month.

There’s a wealth of security features to guard against overpayments, malicious activities, and the time spent having to track it all down.

MineralTree also helps make the payments process more efficient by combining multiple payments into a single electronic file. This can help save a lot of manual labor by cutting down the number of batches AP has to run.


Bookkeeping Software: Timesheets.com
  • Pricing: $3.60/user per month for non-profits. Full plan starts at $4.50/month and goes up to $5.50/month with photos.
  • Rating: 4.1/5 on G2Crowd.
  • Who it’s for: Small to large businesses wanting integrated time-tracking, payroll, and billing.

Timesheets.com tracks employee time and provides a dashboard to manage billing and payroll. They offer a solution for everyone—from freelancers to large-sized businesses.

Employees will like Timesheets.com due to the ease of use. All they need to do is log into the employee portal with their username and password, and they can see their pay stubs and other relevant payroll information.


Finding the right bookkeeping software for your business can be a challenge, especially if you’re not well versed in bookkeeping. We hope the above list helps you narrow down your choices and come to the right decision.

However, if you’re still struggling to find the right tool, don’t have the time, or would rather completely hand it off to someone else, we can help.

At Pilot, our highly experienced team of professional bookkeepers use advanced software tools to automate the aspects of your bookkeeping most prone to human error. Effectively, we let computers do the tedious work while freeing up our bookkeepers to provide a first-class support experience for our clients.

We do all our bookkeeping in QuickBooks Online, which we believe offers the best experience and scalability for our customers. If you like the idea of handing off your books to tech-empowered bookkeepers, Try Pilot Now for one month.

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