Ecommerce bookkeeping built to scale for your business.

Manage your online store cashflow with accurate books and back–office support.

Hundreds of ecommerce companies trust Pilot

pilot custom ecommerce reports

Accurate statements every month

Get a monthly report that includes the metrics that matter: your inventory statement, merchant fees, profit and loss statements, cost–of–goods–sold, income statements, and more. We sync with the tools you already use like Shopify, Amazon, Stripe or Paypal, creating a single source of truth. Our mix of experts and bookkeeping software delivers books with unmatched accuracy.

pilot custom expert support

Personal, expert ecommerce support

Meet your finance expert who knows your ecommerce business inside and out. Together, you’ll establish the right financial foundation, from the best tools to projections. We’re your finance partner from the start.

pilot full claim process handling

One–stop finance shop

Get full bookkeeping and tax help for your online business. With Pilot Tax, we’ll file your taxes and 1099s. Need help with budgets, accounts receivable or payable? We offer these and other additional services to help you make smart business decisions based on your numbers.

The Best in Ecommerce Integrations

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pilot integration bigcommerce pilot integration paypal

Partnering with industry leaders

Pilot partners with the best ecommerce providers for your store’s total financial management.

Frequently asked questions

What kind of ecommerce customers does Pilot support?

Pilot serves ecommerce customers of all shapes and sizes including online-only, multi-channel, and direct-to-consumer brands.

What types of ecommerce platforms do your customers use?

We have customers using every major ecommerce 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 by either the customer or the source of truth for customers’ inventory (e.g. a system like Tradegecko).

What system do you recommend for online store inventory?

We work with a variety of inventory management solutions but recommend Tradegecko and Skubana based on their simplicity of use and ability to scale.

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 ecommerce 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 recommend TaxValet for an end-to-end sales tax solution.

How does Pilot calculate Cost of Goods Sold?

There are three different ways we calculate Cost of Goods Sold (COGS), depending on your business:

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

Does Pilot have the ability to break out Amazon/Shopify fees in the P&L?

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

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

Yes, Pilot can break out your revenue and costs in your Profit & Loss statements by product and/or channel.

Handle all your back-office needs


Stay compliant and up-to-date with Pilot Tax for Ecommerce Businesses. We’ll prepare and file your federal, state, and local income taxes—as well as your 1099s. Plus, get live reminders and status updates about your filings.

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Additional Services

Sometimes you need financial support, beyond monthly bookkeeping. With our additional services, we can help you pay your bills, and create and send invoices to your customers at an hourly rate.

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CFO Services

Need advanced finance support? We have your back. Get the expert CFO support for your business needs, from building budgets to fundraising preparation.

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Ready to get your ecommerce books done right?