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

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 kind of ecommerce customers does Pilot support?

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

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 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 online store 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.

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 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 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 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.

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?