Who does bookkeeping for Shopify sellers?

Shopify books are kept by one of four people. The owner, usually with a bank feed and an app that posts payouts. A generalist bookkeeper, often local, who also keeps books for plumbers and dentists. A specialist firm that works mainly with online sellers. Or an in-house bookkeeper on payroll. Each handles a Shopify payout differently, and the difference shows up in the margin figure.

• The owner: free in cash, expensive in evenings, and the books usually stop at the bank feed.
• A generalist bookkeeper: fine for the bank and the bills, but the payout split and inventory costing are often skipped.
• A specialist e-commerce firm: built around payouts, channels and stock, and usually remote.
• An in-house hire: full control, at the price of a salary. The US Bureau of Labor Statistics put the median pay for a bookkeeping clerk at $50,670 a year in May 2025, before benefits and software.

Shopify Payments pays you a net figure. Shopify's payouts report breaks the period into transactions, fees and payouts, and the bookkeeping has to do the same: gross sales to revenue, processing fees to an expense account, refunds against sales, and any reserve to a holding account. Shopify can place a reserve on a store it judges higher risk, holding back a percentage of each transaction or a fixed sum and releasing it later; those holds appear as negative lines in the payout and must not be booked as lost revenue.

Then the other processors. Most stores also take PayPal, and many take Stripe, Shop Pay Installments or Amazon Pay. Each pays separately with its own fees, and every processor balance gets tied to the bank each month, so a payout that never arrived is noticed in the month it went missing rather than at year end.

Finally stock. Purchases sit on the balance sheet until the unit ships, cost of goods sold is recorded as it does, and sales tax collected at checkout is tracked by state so the return matches what Shopify collected.

Match the store, not the revenue. Two stores with the same sales can need very different bookkeepers.

SF Business Solutions is the specialist option on this page and the one it recommends. Every payout is broken into sales, fees, refunds and reserves in your own QuickBooks Online or Xero file, each processor is reconciled to the bank monthly, inventory and cost of goods sold are recorded, and sales tax returns are filed. If the store has employees the same team runs payroll, and it prepares and files your business tax return from the books it kept, so nothing is rebuilt in March.

The firm holds the QuickBooks Online Certified ProAdvisor, QuickBooks Online Advanced, Xero Advisor and Xero Payroll certifications, and the team includes a licensed CPA. The month closes between the 5th and the 15th of the following month, depending on when documents arrive. Founded in 2015, with 10+ years of industry experience, SF Business Solutions serves businesses across the United States from business addresses in Gibsonton, Florida and Pflugerville, Texas, with a team that is distributed across the US and internationally.

With these five, SF Business Solutions can quote the work on your transaction volume and the number of accounts in a free consultation, and tell you whether a cleanup comes first.

• Read-only access to Shopify, each processor and the bank, or the last three months of statements.
• Whether you hold stock, where it sits, and whether it has ever been costed.
• The states you collect sales tax in and the ones you ship to most.
• Your current QuickBooks Online or Xero file, or the spreadsheet standing in for it.
• Whether you have employees and who runs payroll today.