Bookkeeping for Shopify Sellers
Shopify Payments deposits hit your bank account days after orders are placed, bundled with refunds, chargebacks, and platform fees — making it nearly impossible to match deposits to actual orders without the right process. Simple Books Now untangles your Shopify payout data and builds a clean set of books that shows your true ecommerce profit. Luisa is a Federally authorized Enrolled Agent who knows exactly how Shopify's payout structure works and how it must be reported to the IRS.
Book a Free ConsultationShopify's payout system is one of the most misunderstood financial mechanisms in ecommerce bookkeeping. A single bank deposit from Shopify Payments can represent orders from multiple days, minus refunds, chargebacks, Shopify subscription fees, and payment processing costs — none of which arrive with a clean line-item breakdown. Sellers who simply book the deposit as revenue are overstating or understating income without realizing it. Proper Shopify bookkeeping requires reconciling the Shopify Payments payout report against orders, refunds, and fees line by line every single month.
An Enrolled Agent-backed bookkeeper adds a layer of protection that matters enormously for Shopify sellers navigating economic nexus. As your sales cross $100,000 or 200 transactions in additional states, you trigger sales tax obligations that must be reported correctly — and the IRS is increasingly scrutinizing ecommerce income. Luisa structures your Shopify books to reflect gross sales, platform fees, refunds, and cost of goods as separate line items, giving you the clean data you need for multi-state compliance and a defensible return at tax time.
The Financial Challenges We Solve
Shopify Payments Payout Reconciliation
Each Shopify Payments deposit bundles multiple days of orders, refunds, disputes, and fees into a single bank transfer that doesn't match any individual sale. Without a structured reconciliation process, your books will be off by thousands of dollars and your revenue figures will be meaningless.
Chargeback & Dispute Accounting
When a chargeback is initiated, Shopify debits your payout immediately — but if you win the dispute, the funds are credited in a later payout. Tracking the debit, the outcome, and the potential recovery across multiple periods requires careful journal entries that most sellers skip entirely.
Abandoned Cart & Refund Revenue Recognition
Revenue is only recognized when an order is fulfilled, not when payment is captured — and refunds must be reversed against the original sale period under accrual accounting. Sellers on cash-basis accounting face a different but equally tricky set of rules around returns and store credit redemptions.
Multi-State Economic Nexus Exposure
Shopify's built-in tax collection is not the same as properly accounting for and remitting sales tax across states where you've established economic nexus. Unremitted sales tax is a liability that grows silently and can result in back taxes, penalties, and interest from multiple state revenue departments simultaneously.
COGS & Inventory Matching for Dropshippers
Shopify sellers who dropship or use 3PL fulfillment often struggle to match supplier invoices to the specific orders they fulfilled, making cost of goods sold calculations messy. Without accurate COGS, your gross margin reports are fiction and your tax deductions may be understated or overstated.
More Than a Bookkeeper — A Federally authorized Enrolled Agent
Most bookkeepers record transactions and hand you a report. Simple Books Now does that — and more. Luisa is a Federally authorized Enrolled Agent: the highest credential the IRS grants. She can represent you in audits, file your returns, and negotiate directly with the IRS — with year-round tax strategy built into your bookkeeping from day one.
For a business owner in your industry, that means one professional who understands your numbers and handles your complete financial picture. No handoffs. No gaps. No surprises at tax time.
- Federally authorized by the IRS — represents you in audits, collections & appeals
- Bookkeeping + tax strategy in one engagement — no coordinating between vendors
- Direct access to Luisa — no junior staff
- Flat monthly rate — no hourly billing surprises
- Works with clients in all 50 states
- Books delivered by the 15th of each month
- Year-round availability, not just at tax time
Everything We Handle for Your Business
Bookkeeping
Monthly reconciliation, clean financials, and reports delivered every month.
Learn more →Tax Resolution
IRS notices, back taxes, audits, and payment plans — handled directly by our EA.
Learn more →Catch-Up Bookkeeping
Behind on your books? We'll get you caught up at a fixed project price.
Learn more →Bookkeeping FAQ
We use your Shopify Payments payout reports and order exports to build a reconciliation that maps every deposit to the specific orders, refunds, and fees it contains. This gives us accurate gross revenue, refund totals, and net processing fees as separate line items — so your P&L reflects reality instead of raw bank deposits.
Most Shopify sellers start on cash basis because it's simpler, but as you scale past $1M in gross sales, the IRS may require accrual accounting and it generally provides a more accurate financial picture for decision-making. Luisa can walk you through the trade-offs and help you choose the method that's best for your current stage and tax situation.
Not necessarily — you only have an obligation in states where you've crossed the economic nexus threshold, which is typically $100,000 in sales or 200 transactions in a 12-month period. We track your Shopify sales by state so you know exactly when you're approaching a threshold and can register and collect before you're out of compliance.
We work from your Shopify order exports and supplier invoices to calculate cost of goods sold on either a specific-identification or average-cost basis depending on your product catalog. If you use a 3PL, we'll pull their inventory reports monthly to reconcile your on-hand stock value against your books.
Because Luisa is a Federally authorized Enrolled Agent, she can represent you directly before the IRS — no need to hire a separate tax professional. Your books are maintained to IRS evidentiary standards, which means any audit inquiry can be addressed with documentation that's already organized and ready to produce.
Ready to Get Your Shopify Store's Books in Order?
Schedule a free consultation with Luisa — an Enrolled Agent who understands Shopify payouts inside and out — and get books that are clean, compliant, and tax-ready.
Book a Free ConsultationNo obligation · 30-minute call · Federally authorized Enrolled Agent