Shopify Bookkeeping That Gets Payouts, Fees and COGS Right

The deposit in your bank is not your revenue. We reconcile every payout back to its orders, fees and refunds — so your margin is real and your sales tax is right.

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✓ QuickBooks ProAdvisor Platinum ✓ Xero Platinum Partner ✓ 4.9 from 217 reviews

Shopify makes selling easy and bookkeeping quietly hard. Book the deposit as revenue — the most common mistake we see — and your margin looks better than it is, your sales tax is understated, and your P&L stops being usable for decisions.

What Shopify bookkeeping actually involves

Payout reconciliation

Every Shopify payout tied back to its orders, fees, refunds and adjustments — revenue is gross sales, not net deposits.

Fee separation

Subscription, transaction and payment fees booked as expenses — not netted invisibly out of sales.

Inventory & COGS

Cost of goods matched to sales so margin is real. “Expense it when purchased” makes good months look bad and bad months look fine.

Sales tax

Multi-state nexus tracked, collected tax booked as a liability (it is not income), filings supported.

Multi-channel

Amazon, Etsy or POS alongside Shopify? Each channel reconciled separately, one clean consolidated P&L.

Monthly close

Bank and card reconciliation, P&L and balance sheet delivered on a fixed day each month.

Signs your Shopify books are wrong right now

QuickBooks revenue doesn’t match Shopify’s sales reports. A growing “Shopify” or “Uncategorized” catch-all account. Sales tax sitting in income. Inventory unchanged on the balance sheet for months. Refunds showing up nowhere. Any one of these misstates margin and taxes — we find at least one in roughly a third of the Shopify accounts we take over.

How we work

QuickBooks Online or Xero connected to your store, a real accountant on your account — not software you configure yourself. Fixed monthly pricing quoted after a short call based on order volume and channels; see packages. Behind on the books? Catch-up and QuickBooks cleanup come first at a fixed quote, so monthly service starts on clean numbers.

Find out what your Shopify books are hiding — free

View-only access to QuickBooks or Xero in, a plain-English error list back within 48 hours.

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Common questions

Do I need A2X or another connector app?

Sometimes — and sometimes it’s an unnecessary subscription. We wrote an honest breakdown: A2X vs manual reconciliation.

Can you handle Shopify plus Amazon?

Yes — each channel reconciled on its own, one consolidated P&L. See Amazon seller bookkeeping for how settlements are handled.

My books are months behind. Where do I start?

With the free review — it tells you exactly what the backlog involves. Then a fixed-quote catch-up project, then monthly service.

Cloud Accountants LLC — Colorado-registered, QuickBooks ProAdvisor Platinum, Xero Platinum Partner, 4.9 from 217 reviews, 200+ US businesses served.
Related: Ecommerce & DTC bookkeeping · Amazon seller bookkeeping · How to hire a bookkeeper · Contact us