Catch-Up Bookkeeping for E-commerce
Selling on 3 platforms with 400 transactions a month? We'll untangle it all.
Multi-state sales tax, COGS you haven't tracked since last summer, and platform fees everywhere. We catch up e-commerce bookkeeping in 3-7 days for $69-$99 per month of catch-up.
See My Price →Takes 2 minutes · No card required
Why E-commerce Bookkeeping Falls Behind
The Volume Problem
Hundreds of transactions daily across multiple accounts — sales, shipping, fees, refunds, advertising, inventory. Each one needs categorization, and the volume never lets up.
The Multi-Platform Problem
Shopify, Amazon, Etsy — each has its own payout schedule, fee structure, and reporting format. Reconciling them into one QBO file is a puzzle.
The Sales Tax Problem
Selling across state lines means sales tax nexus in multiple states. Without bookkeeping, you don’t know what you owe.
The Inventory Problem
COGS is critical for profitability but notoriously hard to track. Every sale needs matched to its inventory cost.
We sell on Shopify and Amazon. Reconciling platform deposits against actual sales was a nightmare. Ketchup's AI matched everything in 3 days.
— Marcus T., DTC Brand Owner
What Catch-Up Covers for E-commerce
Multi-platform reconciliation, fee breakdowns, and COGS tracking — so you know your real margins.
Multi-Platform Reconciliation
- ✓Shopify payouts matched to orders
- ✓Amazon disbursements mapped to fees/net revenue
- ✓Etsy deposits reconciled with listing/transaction fees
- ✓Stripe/PayPal matched to orders
Fee Categorization
- ✓Platform referral/listing fees
- ✓Payment processing fees
- ✓FBA fulfillment fees
- ✓Advertising/PPC charges
- ✓Monthly subscription fees
COGS Tracking
- ✓Inventory purchases categorized
- ✓Shipping costs to warehouse
- ✓Packaging materials
- ✓Returns and damaged goods adjustments
Sales Tax Reconciliation
- ✓Tax collected by platform
- ✓Tax you owe by state
- ✓Nexus tracking
- ✓Marketplace facilitator tax
Deductions E-commerce Sellers Miss
For a seller doing $300K in revenue, missed deductions easily total $15,000-$40,000 — representing $3,750-$10,000 in unnecessary taxes.
| Deduction | Typical Annual Amount |
|---|---|
| Platform fees (Shopify, Amazon, Etsy) | $5,000-$50,000+ |
| Payment processing fees | $3,000-$30,000+ |
| Shipping supplies and postage | $2,000-$20,000+ |
| Advertising (PPC, social, influencer) | $5,000-$100,000+ |
| Software (inventory, analytics) | $1,000-$10,000 |
| Home office (if applicable) | $1,500-$5,000 |
Cost Comparison (12 Months Behind)
| Option | Cost | Timeline |
|---|---|---|
| Accounting Ketchup | $948 | 5-7 days |
| Bench | $4,740-$6,588 | 4-6 weeks |
| E-commerce specialist CPA | $5,000-$15,000 | 4-8 weeks |
| DIY | $0 + 50-100 hours | Months |
Frequently Asked Questions
Can you handle Amazon FBA bookkeeping?
Yes. We reconcile Amazon disbursement reports with your bank deposits, categorize FBA fees, and separate advertising charges from fulfillment costs.
Do you support Shopify?
We work with QuickBooks Online, where your Shopify data ultimately lives. If you have Shopify connected to QBO, we categorize everything that flows in.
I sell on Amazon, Shopify, AND Etsy. Is that a problem?
Not at all. Multi-platform sellers are common in our client base. We reconcile each platform’s deposits separately and categorize everything into a unified QuickBooks file.
Do you handle sales tax filing?
No. We categorize and track sales tax collected and owed, but actual sales tax filing should be done through a service like TaxJar, Avalara, or your CPA. Clean books make sales tax filing straightforward.
How We Approach E-commerce Bookkeeping
E-commerce bookkeeping isn't like other small business bookkeeping. The multi-channel complexity, high transaction volume, and platform-specific fee structures require a specialized approach.
Multi-Channel Revenue Reconciliation
Selling on Shopify, Amazon, and Etsy means three different payout schedules, three different fee structures, and three different reporting formats. We reconcile each platform's deposits against actual orders — matching gross sales, fees, refunds, and net deposits to your bank. See how our process handles this.
COGS Tracking & Inventory
Your true profit isn't revenue minus expenses — it's revenue minus COGS minus expenses. We track inventory purchases, shipping to warehouse, packaging materials, and returns/damaged goods so your P&L shows real gross margin, not inflated numbers.
Sales Tax Nexus
If you sell across state lines (most e-commerce sellers do), you may have sales tax nexus in multiple states. We track tax collected by platform vs. tax owed by state, giving you clean data for services like TaxJar or Avalara.
Platform Fees & Advertising
Amazon referral fees, Shopify subscription fees, Etsy listing fees, payment processing, FBA fulfillment, PPC advertising — these are all deductible, but they need to be correctly categorized. Lumping them together as “fees” makes your financials useless. We break them out properly.
Returns & Refunds
E-commerce return rates run 15-30%. Each return creates a revenue reversal, a potential inventory adjustment, and sometimes a restocking fee. We ensure returns are properly netted against revenue so your financial statements reflect actual sales.
“We sell on Shopify and Amazon. Reconciling platform deposits against actual sales was a nightmare. Ketchup's AI matched everything in 3 days.”
Marcus T.
DTC Brand Owner
From the Blog
QuickBooks Cleanup vs Catch-Up Bookkeeping
"Cleanup" and "catch-up" sound like the same thing. They're not. Here's the difference — and how to know which one you need.
Read articleHow Much Does Catch-Up Bookkeeping Cost?
What does it actually cost to get your books caught up? We break down pricing across every option — from DIY to CPA — with total cost tables for 3, 6, 12, and 24 months.
Read articleKnow your real numbers.
Clean books reveal your actual margins, your real COGS, and where your money is actually going.