Frequently asked questions

Pilot aims for accuracy and transparency in both our books and how our service works. If anything remains unclear or if you have a question not covered in this FAQ, please send us a message and we will happily get you the answers you need.

How It Works

How does pricing work?

Our bookkeeping and tax plans are based on an annual subscription model with transparent pricing that scales with your expense rate and your business needs such as connected institutions, bills, and invoices. See our pricing page for more details.

Is support included? Can I ask questions?

Yes! Support is included in your plan. Your dedicated finance expert is happy to answer any questions you might have. We strive to respond to inquiries in a business day or less. See our pricing page for more details.

Will you send invoices to my customers and help pay my bills?

Yes, we’re happy to provide this support as an additional service. Please contact your sales rep for details.

What’s the difference between accrual and cash bookkeeping?

Cash bookkeeping only tracks when money enters or leaves a bank account. Accrual bookkeeping is a more sophisticated approach that records when the money was earned or owed. Most larger companies use accrual and Pilot does accrual from day one so there’s no painful transition later.

What types of companies can Pilot serve?

We have over a thousand customers ranging in all sizes and spanning many industries. We specialize in working with high-growth technology startups, ecommerce providers, professional services, non–profits and more. Get in touch with us to see if Pilot is the right fit for you.

What are the requirements to start with Pilot?

We have three requirements that allow us to deliver the most accurate books for your business.

  1. Electronic transaction access
  2. Expense reporting software
  3. No commingling of personal expenses
Do you support international companies?

We can support you if your company is a US entity, no matter where you are based in the world. We can also provide US entities with foreign subsidiaries with consolidated reporting. As of now, we do not support foreign entities.

Are AP/AR services included in Pilot Bookkeeping?

They are not included by default, but you can add them to any plan. Please ask your sales rep for details.

Do you do bookkeeping for companies with NSF SBIR grants?

Yes, we support bookkeeping for companies who’ve been awarded SBIR grants. Pilot has deep expertise in working with complex SBIR bookkeeping requirements, such as dealing with indirect costs, unallowable expenses, and more.


How do prices change as I grow?

We understand the importance of predictability and transparency. Every month, we’ll average your prior 3 months of books to understand your current expenses, as well as how your financial institution connections, special transactions, and hours of support have changed.

How should I calculate my monthly expenses? What does that include?

For pricing purposes, we include in expenses the money your company spends each month, including payroll, cost of goods sold, and distributions.

Why do you price based on expenses?

Our goal is simple and transparent pricing. In examining different models, we found that expenses closely reflected business complexity while also having the advantage of being simple to calculate. To determine the best Pilot plan for your business’ needs, we also factor in the number of financial institutions, transactions, and hours of support.

What is your cancellation policy? What if I prepaid for the year?

Your subscription will continue until the end of your billing cycle. If you decide not to renew after the year is over, you can let us know in advance and we’ll stop billing you for the next cycle.

When I prepay for a year, does that lock in my price?

No, if your business is growing rapidly, your books are growing in complexity as well. If your expenses and other support needs change and exceeds the amount you’ve prepaid for, you’ll get billed the difference that month.

Are there any one–time fees when I sign up for Pilot?

Yes, there’s an onboarding charge equal to one month of bookkeeping to help us make sure your setup process is a smooth one.


Why use QuickBooks?

Pilot does all of its bookkeeping in QuickBooks Online because it offers a number of advantages:

  • Seamless tax prep. Virtually every tax preparer in the US knows how to work with QuickBooks. You’ll have the freedom to choose any tax preparer you want.
  • Industry standard. In addition to tax preparers, most other financial professionals (e.g., attorneys, bankers, and venture capitalists) all know how to work with QuickBooks. Again, this gives you the most freedom when making financial decisions.
  • Data portability. QuickBooks means you’re not locked in. If you ever decide to move on from Pilot, your data goes with you, in a format that is immediately useful.
If I’m on Xero, can you migrate me from Xero?

Yes, we can help you transition your books over to QBO. As part of our onboarding process, we’ll make monthly journal entries in Quickbooks from your monthly account totals in Xero (for both the balance sheet and the P&L/income statement) going back to the beginning of the year.


How do taxes work with Pilot?

You have a couple of options for doing your taxes when you use Pilot.

The first option is to use Pilot Tax. Please note that tax preparation is not included in your Pilot Bookkeeping subscription – you must purchase Pilot Tax for those services.

The second option is to use a firm of your choice and have Pilot hand off your prepared books to them. This handoff is included in your Pilot Bookkeeping subscription at no additional cost.

What does Pilot Tax include?

Pilot Tax includes federal, state, and city level income tax preparation, Form 1099-NEC e-filing services, and email support for included deliverables. Please see the full scope of services here.

If Pilot didn’t do my books for the entire year, can I still use Pilot Tax?

Yes, we’ll generally want to take a look at the year’s books to make sure they meet our standards, but many of Pilot Tax customers started Pilot halfway through the year.

Do you do personal income taxes?

At this time, Pilot does not file personal income taxes.

Can Pilot handle my 1099s?

If you have Pilot Tax, our 1099 vendor information request form makes it easy to submit vendor information and e-file Form 1099-NEC. If you are only using Pilot Bookkeeping, we are not able to file 1099 forms for you.

R&D Credit

Do I qualify for R&D tax credits?

If your business has less than $5 million in annual revenue, and it's been less than five (5) years since your first gross receipts/sales, you can frequently reduce your Social Security Payroll tax liability under the PATH Act R&D credit. If you do not qualify under the PATH Act R&D Credit, you can take regular R&D Credit against income taxes (rather than against payroll taxes).

What activities qualify for R&D tax credit?

Qualifying R&D expenses and/or activities are those which pass this four-part test:

  • Technical uncertainty. The activity is performed to eliminate technical uncertainty about the development or improvement of a product or process, which includes computer software, techniques, formulas, and inventions.
  • Process of experimentation. The activities include some process of experimentation undertaken to eliminate or resolve a technical uncertainty. This process involves an evaluation of alternative solutions or approaches and is performed through modeling, simulation, systematic trial and error, or other methods.
  • Technological in nature. The process of experimentation relies on the hard sciences, such as engineering, physics, chemistry, biology, or computer science.
  • Qualified purpose. The purpose of the activity must be to create a new or improved product or process, including computer software, that results in increased performance, function, reliability, or quality.
How large will my R&D tax credit be?

Unlimited, if applying the R&D credit against income taxes. These credits can range between 5% and 15% of qualifying R&D costs. If taking the PATH Act R&D credit, a company can receive up to $250k* against payroll taxes and take the remainder against income taxes.

As an example, for an unprofitable 5-person tech startup that has less than $5M in annual revenue with roughly 80% of time being spent on qualifying R&D activities, and average salary of $100k/year, the credit might be between $20k to $60k. Pilot’s fee is a small percentage of the total qualifying R&D expense and easily pays for itself by securing the R&D Tax Credit for you.

*$500,000 for 2023 tax year, $250,000 for 2022 tax year

Can I claim the R&D credit retroactively?

Yes, we can help you file an amended tax return to claim the R&D credit for previously filed Income Tax returns (past 3 years), but you cannot take the PATH Act R&D credit on an amended tax return.

What does Pilot R&D Credit Service include?

We help businesses with all aspects of claiming these R&D Tax Credits. Pilot will:

  • Identify and calculate qualifying R&D expenses
  • Prepare Forms 6765, 8974, and 941 to gain IRS approval of credit. If you use Pilot Tax, we’ll file on your behalf as well.
  • Prepare all required supporting technical and financial documentation, including documentation of research time, R&D payroll expenses, etc. This is an important pre-requisite to support an IRS audit in case that happens.
  • Coordinate with your tax preparer, payroll provider, and accountant to ensure your books and taxes are accurate
  • Continually ensure the credit is applied correctly against your payroll liabilities
  • Email and phone support with R&D credit experts
Does Pilot support you in case of an audit?

Yes, we can help support you in the case of an audit. For more details, please contact us.

Why is having an R&D study done important?

Pilot recommends anyone who claims the R&D credit to get a study done. An R&D study determines the total amount the business should claim and collects the necessary documentation to support that claim.

When filing for the R&D tax credit, you must submit the relevant tax forms to the IRS. However, you must also have the technical and financial justification of what you were claiming prepared in case the IRS audits your claim. If the IRS audits the claim and you can’t produce technical and financial evidence behind what you claimed, you will need to return the money and potentially pay a penalty. The R&D Tax program is on the IRS’s "Dirty Dozen List". Once you’ve been audited, the IRS can also audit your claims for up to 7 years prior – so you need to make sure that each year’s claim has proper and thorough substantiation.

Can I use Pilot R&D Credit service without using Pilot Tax?

Yes, we’ll calculate the R&D tax credits and provide the necessary documentation for your tax preparer to file. If you use Pilot Tax, we’ll take care of the full process and file the necessary tax paperwork on your behalf as well.

Are there state-level R&D tax credits?

33 states currently offer an R&D credit. Generally, the states follow federal guidelines on what constitutes qualified R&D expenditures with few exceptions. Pilot will provide guidance on state level credits. For example, the CA R&D credit is non-refundable which means it cannot be taken against payroll tax. Work must be done in CA to be considered qualified and CA credits can carry forward indefinitely until exhausted.

CFO Services

When should I outsource vs. hire a full–time CFO?

You should outsource CFO services in two situations:

  1. If you are a small, growing business where you don’t have many needs or ability to pay for a full-time CFO, or
  2. If you are a large business that only needs CFO services occasionally.
What does the process for Pilot CFO Services look like?

Get started by filling out the form here. Our account executives will set up a call to discuss what fits your business needs and answer any questions. After you sign up, our CFO team will further scope out the details of supporting your financial needs and timelines during a kickoff call. Our goal is to deliver robust financial analysis and expert support to unlock growth for your business. For more details on our CFO Services, see here.


Why is bookkeeping for consumer and retail companies unique?

Online retailer and consumer companies face challenges around managing physical goods (such as COGS, inventory, supply chain, fulfillment), and often have complex selling channels (such as multiple platforms, differing fee and payout structures, and multiple payment processors). They also tend to have large transaction volumes. All of these things affect your books, which is why it’s important to have a bookkeeper with a strong background in your industry.

What kinds of consumer and retail customers does Pilot support?

Pilot serves consumer and retail customers of all shapes and sizes, across different sectors (food and beverage, apparel, hard goods) and business models (direct-to-consumer and multi-channel retailers, manufacturers, wholesalers).

What types of sales platforms do your customers use?

We have customers using every major e-commerce platform, including Shopify, Amazon, WooCommerce, Magento, BigCommerce, and Salesforce Commerce Cloud.

Do you handle inventory?

Pilot makes inventory updates in your financial statements every month based on data provided either directly by you or by the source of truth for your inventory, such as an inventory management system (e.g., TradeGecko / Quickbooks Commerce).

How does Pilot calculate Cost of Goods Sold?

There are several different components that make up Cost of Goods Sold (COGS) for a typical Consumer and Retail company:

For product COGS (i.e., the actual cost of the items sold), we base our calculations on inventory and fulfillment information you share with us.
For Merchant Fees and Shipping Costs, we track your metrics automatically and categorize your variable expenses in COGS.
For all other variable costs you wish to track as COGS (e.g., Storage Costs), we work with you to create accounts and categorization rules to implement this for your business.

What system do you recommend for managing inventory?

We work with a variety of inventory management solutions but recommend TradeGecko/Quickbooks Commerce and Skubana based on their simplicity of use and ability to scale. Read more about our recommended technology stack for growing retailers here.

How does Pilot handle returns/gift cards?

Our automation pulls this information directly from your store, ensuring you have accurate figures for both items month–over–month.

Yes, Pilot can separate our merchant fees of all types in your Profit and Loss statements.

Yes, Pilot can separate our merchant fees of all types in your Profit and Loss statements.

Does Pilot break out revenue and costs by product and/or channel?

Yes, Pilot can break out revenue and costs in your P&L by product line and/or channel. Depending on the degree of granularity you’d like to capture, we recommend doing this in the P&L itself for simpler break-outs (e.g., revenue by channel) and via a detailed KPI dashboard for more complex analysis (e.g., monthly profitability by SKU).

Your Core plan includes connections to four financial institutions, but my business uses more than four. Does that mean I'm a Plus customer?

For simple consumer and retail companies that have more than 4 financial institutions, we offer the option of adding additional financial institutions to your Core subscription for a flat fee.

Does Pilot handle sales tax?

We don’t currently offer sales tax services, but can recommend a number of software and service providers depending on your needs.

Can Pilot help me manage KPIs that aren’t in the books?

Yes, we offer KPI tracking and dashboards through CFO Services. For Consumer & Retail clients, our CFO Services team typically helps track KPIs such as marketing metrics throughout the customer funnel, LTV/CAC, inventory turns, and profitability across the product portfolio.

Can Pilot help me raise capital?

Yes, through the Fundraising Strategy & Support package offered by our CFO Services. Our experienced CFOs can assist with strategy, pitch narrative and deck development, financial and market analyses, and more.

See what Pilot can do for you

Get the peace of mind that comes from partnering with our experienced finance team.

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