How to automate your bookkeeping (without doing it all yourself)

A lot of companies say they offer “automated bookkeeping.” Usually, that means they’ve automated a sliver of it—maybe categorizing expenses or syncing a bank feed. But true end-to-end automation? That’s not happening with one app.

The good news: you can absolutely automate your bookkeeping. You just need the right mix of tools and support to handle everything from expense tracking to reconciliations to getting paid.

If you set it up right, the system mostly runs itself. You’ll spend less time chasing receipts and more time acting on clean, accurate financials. And yes, it works whether you're on cash or accrual.

In this post, we’ll break down what automated bookkeeping actually means, what needs to be in place to make it work, and why it’s worth setting up—before walking through the tools we use to make it happen.

At Pilot, we have a team of expert bookkeepers (with software superpowers) doing your books in QuickBooks Online. Let us take the bookkeeping burden off your plate: Try Pilot's Bookkeeping Services Now.

What are the benefits of bookkeeping automation?

Bookkeeping might not be your biggest pain point. But it’s one of the easiest to clean up if you use the right tools.

Automating your bookkeeping helps you:

• Save time every month
• Reduce human error (and cleanup later)
• Stay tax-ready year-round
• Make faster decisions with up-to-date data
• Focus your team on growth—not admin
  
  

And maybe most importantly: automation lets you stay on top of your finances without needing to be a finance person. You’ll always know where the money is going, what’s working, and what’s not.

Why you can’t automate your bookkeeping with just one tool

Bookkeeping isn’t a standardized service. There’s no one-size-fits-all list of tasks that a bookkeeper will do, although there are more or less common services offered. It’s always important to discuss what you want your bookkeeper to accomplish before making a hire. In general, bookkeepers will do some or all of the following:

• Categorizing transactions
• Reconciling accounts
• Creating financial statements
• Managing bills and invoices

Some bookkeepers will handle all four. Many won’t. And even when they do, smart automation can multiply their impact leading to faster closes, fewer mistakes, and more time spent actually helping your business.

That’s why we recommend building a stack:

• One tool to house your books
• One to automate expense tracking
• One to handle what software can’t
• One to simplify getting paid and paying others
  

We also include an optional fifth for payroll and HR automation—b

Step 1:  Choose bookkeeping software that can handle growth

Every automation stack needs a home base. Your bookkeeping software is where all your financial data lands, gets categorized and turns into reports. It’s also where the other tools in your stack sync and store their info—so this choice matters.

You don’t need the flashiest tool. You need something reliable, scalable, and compatible with the rest of your workflow.

For most businesses, QuickBooks Online checks those boxes. It handles both cash and accrual accounting, plays well with tools like Expensify and Bill.com, and gives your bookkeeper a clear place to work.

Not sure what’s right for you? We put together a guide comparing QuickBooks, Xero, and Wave—so you can pick the best fit for your business, not just the most popular name.

Step 2: Automate expense tracking  

If your business has almost no expenses, you might not need this. But if any of the following apply, it’s worth automating this part of your workflow:

• You manage inventory
• You travel for work
• You buy supplies or equipment
• You entertain clients
  

Bookkeepers can’t track your expenses for you. They can’t see your credit card or guess if that Uber was personal or business. The cleaner your records are upfront, the more accurate your books will be later.

That’s where Expensify comes in. It turns receipts into real-time reports and syncs directly with QuickBooks.

Here’s how it works:

• Snap a photo of your receipt
• Approve or reject in one click
• The data flows straight into your books
• Reimbursements happen automatically
  

It’s not magic. But it’s close. And it saves hours you’d otherwise spend sorting through emails, statements, and spreadsheets.

Step 3:  Automate the bookkeeping process (with help)

QuickBooks doesn’t close your books on its own. It’s a tool, not a bookkeeper. If you want automation that works end to end, you need the right blend of software and human oversight.

Here’s the reality:
Every month, someone has to make sense of how money moved through your business. That means reviewing bank statements, credit cards, payroll runs, invoices, and more. Some of that work is repetitive and easy to automate. Some of it isn’t.

That’s why we built Pilot the way we did.
We use automation to handle the repeatable, error-prone parts—so our bookkeepers can focus on the exceptions, the edge cases, and the questions that actually require judgment.

The result:

• Clean, accurate books in QuickBooks Online
• Monthly financial statements (P&L, balance sheet, and cash flow)
• A dedicated expert you can contact when something doesn’t add up
  

Whether you’re prepping for a raise or planning next year’s budget, you’ll have numbers you can trust—and a team that explains them.

Step 4: Automate accounts payable & receivable  

With the right setup, you can automate most of your accounts payable (AP) and accounts receivable (AR) workflows: sending invoices, routing approvals, syncing payment data, and updating your books.

We recommend Bill.com. It streamlines both sides:

• Sends invoices and payment reminders automatically
• Manages bill approvals with a simple click
• Syncs payment data directly to QuickBooks
  

You still need to review and approve the right things—but the platform handles the repetitive tasks. That means fewer missed payments, faster collections, and less back-and-forth between tools or team members.

Paired with QuickBooks, Expensify, and Pilot, Bill.com rounds out a stack that automates your back office without losing control.

(Bonus) Step 5: Automate payroll and benefits

Most bookkeepers don’t handle payroll or HR—and they shouldn’t have to. But if you’re trying to build a back office that runs smoothly, this is one more area where automation pays off.

We recommend Gusto. It simplifies payroll, tax filings, and benefits admin for small businesses and startups.

Here’s what it covers:

• Run payroll in minutes
• Automatically file and pay payroll taxes
• Manage employee benefits like healthcare and 401(k)
• Stay compliant without chasing deadlines

Gusto doesn’t automate everything, but it gets the busywork off your plate. If you’re growing past a few employees—or just tired of running payroll manually—it’s a smart add-on to your stack.

The automated bookkeeping stack we recommend 

Automated bookkeeping doesn’t require a dozen tools. It requires the right ones, working together. This is the stack we rely on at Pilot and recommend to every business we work with.

• QuickBooks Online
  Bookkeeping platform
  Tracks all financial activity and integrates with the full stack.
• Expensify
  Expense tracking + categorization
  Captures spend in real time and automates classification.
• Pilot
  Human-powered bookkeeping + review
  Reconciles, reports, and handles the edge cases software can’t.
• Bill.com
  AP/AR automation
  Automates invoices, bill pay, and approvals.
• Gusto (optional)
  Payroll and benefits
  Runs payroll, files taxes, and manages benefits in one place.

Want Help Putting It All Together?

Bookkeeping automation isn’t about finding the perfect app, it’s about building the right system. With the tools above, you can offload the repetitive work, reduce errors, and finally get books you can trust.

It won’t run itself completely. But when you combine smart software with human expertise, it gets pretty close.

Want help getting it up and running? Talk to our team. We’ll help you build it and keep it running smoothly.