E-Commerce Bookkeeping Services for Online Stores
Multi-channel sales reconciliation and inventory cost tracking are eating your time. Twelix fixes your books and keeps them clean so you can focus on scaling your store.
Mistakes e-commerce owners make with their books
These aren't rare edge cases — they show up in almost every new client account we onboard.
Counting gross revenue as income
Overstating profit by including marketplace fees, shipping costs, and refunds
We reconcile net payouts and separate fees, refunds, and actual revenue
Ignoring multi-state sales tax nexus
Penalties and back-taxes when states audit your marketplace sales
We track nexus thresholds across all states where you sell
Not tracking COGS by SKU or product line
No visibility into which products are actually profitable
We set up COGS tracking at the product or category level
Are these showing up in your books right now?
Get a Free Books ReviewWe'll tell you exactly what we find — no charge.
E-Commerce Bookkeeping Challenges
Multi-Channel Complexity
Shopify, Amazon, Etsy, eBay — each platform has different payout schedules, fees, and reporting formats.
Sales Tax Nightmare
Multi-state nexus, varying tax rates, and marketplace facilitator laws make compliance overwhelming.
COGS Tracking
Properly tracking cost of goods sold across product lines and suppliers requires precise inventory accounting.
Payment Processor Reconciliation
Stripe, PayPal, Shopify Payments — reconciling payouts with fees and refunds is time-consuming.
Our E-Commerce-Specific Services
Twelix assigns you a bookkeeper with deep e-commerce expertise. Not a generalist — a specialist who knows your business model.
Numbers that actually tell you how your e-commerce business is performing
If your current books can't surface these, you're flying blind.
Gross Margin by Channel
Revenue minus COGS per sales channel
Shows which platforms are actually profitable after fees
Customer Acquisition Cost
Ad spend divided by new customers
Tells you if your marketing spend is sustainable
Return & Refund Rate
Returns as % of gross sales
Flags product quality or listing accuracy issues early
Your bookkeeper should be surfacing these every month.
See How We ReportTools We Work With
E-Commerce tax deductions our bookkeeping service tracks for you
These write-offs are built into how we categorize your expenses from day one — so nothing slips through at tax time.
Shipping & Fulfillment
Postage, packaging materials, 3PL warehouse fees, and shipping insurance
Software & Subscriptions
Shopify, Amazon Seller fees, email marketing tools, and analytics platforms
Product Photography
Studio costs, photographer fees, and editing software for product listings
Home Office
Portion of rent, utilities, and internet if you run your store from home
Advertising Spend
Facebook Ads, Google Shopping, influencer partnerships, and PPC campaigns
Returns & Damaged Goods
Write off unsellable returned inventory and damaged products
Every one of these is included in how we run your books.
See What's Included in Your PlanFlat monthly rate · No contracts · Start in 48 hrs
Why E-Commerce Businesses Choose Twelix
We don’t just keep your books — we give you the financial clarity to run your e-commerce business with confidence.
Dedicated bookkeeper with e-commerce and DTC expertise
Multi-channel reconciliation handled automatically every month
Sales tax nexus tracking across all 50 states
COGS and inventory cost tracking built into your monthly reports
24-hour response time on all communications
E-Commerce Bookkeeping FAQ
Yes. We reconcile revenue from Shopify, Amazon, Etsy, eBay, and other platforms into a single, accurate set of books.
We track your sales tax nexus obligations and ensure your books reflect the correct tax liabilities. For filing, we coordinate with your tax advisor.
Returns, refunds, and chargebacks are reconciled monthly so your revenue figures are always accurate.
Yes. We integrate with A2X, Shopify reports, Amazon Settlement reports, and other e-commerce accounting tools.
Absolutely. We set up and maintain cost of goods sold tracking for your entire product catalog.
What our e-commerce bookkeeping service covers — already
These aren't questions you need to bring to a meeting with us. They're already built into how our service works.
We reconcile every sales channel separately
Shopify, Amazon, Etsy, and every other platform reconciled individually before consolidating into your P&L — so your revenue figures are always channel-accurate.
We track COGS at the product or category level
Product-level or category-level cost of goods tracking is set up from day one — so you see true margins on every item, not just blended averages.
We account for marketplace fees, refunds, and chargebacks separately
Fees, refunds, and chargebacks are broken out individually so your gross revenue and net revenue are always distinct and accurate.
We monitor sales tax nexus across all states
We track your nexus thresholds across every state and flag when you cross registration requirements — before it becomes a liability.
We reconcile payment processor payouts, not just sales totals
Every Stripe, PayPal, and Square payout is reconciled to the transaction level — not just the deposit amount.
All of the above is already built into every Twelix engagement — and we can show you on your first call.
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Ready to Fix Your E-Commerce Books?
Book a free consultation. We will review your situation and give you a firm quote within 24 hours. No sales pressure.