Messy ecommerce books usually share the same problems. Shopify or Amazon deposits hit the bank as net payouts, but nobody recorded the gross sales, refunds, fees, and sales tax that made up those deposits. Inventory was never tracked properly. Sales tax was collected but never reconciled to what was filed. QuickBooks Online has months of transactions sitting in “Uncategorized Income” or matched to the wrong accounts. Catch-up work fixes all of that before a tax return gets filed on numbers that don’t reflect reality.

The starting point is platform exports. Pulling full transaction reports from Shopify, Amazon, Etsy, Walmart, or whichever channels you sell on gives the actual gross sales, discounts, refunds, shipping income, and marketplace fees by month. Without these reports, the books only show net deposits, which understates revenue and hides deductible expenses like merchant fees and platform commissions.

Payout reports come next. Each deposit that hit the bank needs to be tied back to a specific payout period from the platform. That payout includes sales, refunds, chargebacks, fees, holds, and sometimes sales tax remitted on your behalf. Matching the bank deposit to the payout detail is what turns a single lump sum into accurate revenue, expense, and liability entries.

Sales tax reports get reconciled against what was actually filed and paid. For marketplace facilitator states, the platform collected and remitted, and that has to be recorded correctly so it doesn’t double up as revenue or get missed as a liability. For states where the seller files directly, the catch-up needs to confirm what was collected, what was filed, and whether there are unfiled returns that need attention.

Inventory records get rebuilt or reconciled depending on what’s available. If you use Cin7 Core, SOS Inventory, or Shopify’s native inventory, the cost of goods sold and ending inventory values need to tie to actual counts. Without this, gross margin is a guess and the tax return overstates or understates income.

Finally, the QuickBooks Online file itself gets cleaned up. Duplicate transactions, miscategorized expenses, owner draws coded as expenses, transfers showing as income. All of it gets corrected so the financials are usable.

GMJ prices catch-up work as a project based engagement because every situation is different. A six-month cleanup for a single Shopify store is not the same as two years of multi-channel selling with inventory that was never tracked. You can read more about our catch-up bookkeeping approach, or learn about our small business accounting, bookkeeping and tax services in Jacksonville, NC if you want a broader picture of how we work with ecommerce sellers year-round.