Bookkeeping for online sellers

Shopify accountants and bookkeepers

A Shopify store can receive money through Shopify Payments and other payment gateways. Choose a firm that can account for each payment source without counting an order or bank deposit twice.

Services checked against firm websites on October 8, 2026. Confirm availability, fees, and service region with each firm. Inclusion does not certify a firm or establish a Taxomate partnership.

T-Count

Confirm service region with the firm

Ecommerce accounting for Amazon, Shopify, Etsy, and BigCommerce sellers using QuickBooks Online or Xero.

Accounting software
QuickBooks Online, Xero

Check the firm's published services

Ask for a payment-source map

A store has $1,000 in sales: $800 paid through Shopify Payments and $200 through another gateway. Ask the firm to show both settlement paths and confirm that the bank deposits clear those balances rather than create another $1,000 in sales.

  • Which payment gateways will you reconcile besides Shopify Payments?
  • How do you account for refunds that settle after the original sale?
  • How do you keep Shopify bills separate from fees deducted from payouts?
  • How do you review payment clearing balances at month end?

These are simplified discussion examples. Your settlement reports and accounting policy determine the actual entries.

Check fit before you hire

Ask whether the proposal includes monthly reconciliation, cleanup, tax filings, and inventory work. Confirm your accounting system and the integration the firm uses. A firm's marketplace experience does not mean it uses Taxomate.

Keep the account in your business's name. Agree on access, review dates, deliverables, and how unresolved payout differences will be handled.