How to Find a Shopify Accountant or Bookkeeper [2026 Guide]

Managing your Shopify store finances can quickly become overwhelming.

Many merchants start out doing their own bookkeeping, then realize a specialized Shopify accountant or Shopify bookkeeper can help them save time, reduce errors, and unlock better cash flow and profitability insights.

In this guide, you’ll learn how to find a Shopify accountant who fits your business, which questions to ask to confirm their expertise, and what “Shopify-specific” expertise to look for.

Key takeaways:

• The A2X Ecommerce Accountant & Bookkeeper Directory is the quickest and easiest way to find a vetted accountant who understands Shopify and ecommerce bookkeeping workflows.
• A specialized Shopify accountant understands Shopify Payments payouts, fees, refunds, chargebacks, bulk payout reconciliation, payment gateway reconciliation, and sales tax and VAT/GST considerations.
• This guide covers signs it’s time to hire a Shopify accountant or bookkeeper, skills and expertise to look for, and how to find the accountant/bookkeeper for your Shopify store.

Watch this video to learn more about the A2X Ecommerce Accountant & Bookkeeper Directory.

Why do Shopify merchants need a specialized accountant?

Running a Shopify store creates accounting and tax complexity that many generalist accountants don’t see every day, especially when you’re dealing with Shopify Payments, third-party processors like PayPal and Stripe, and multi-channel selling.

A specialized Shopify accountant supports:

• Accurate ecommerce bookkeeping (revenue recognition, refunds, etc.)
• Consistent month-end close and clean financial statements
• Better inventory and COGS visibility
• Sales tax, VAT, and GST compliance planning
• Channel profitability analysis (Shopify vs Amazon, Etsy, wholesale, POS)

Generalist accountant vs. Shopify accountant

A generalist accountant supports many industries and may not be fluent in Shopify’s payout structure, payment processing fees, and reconciliation workflow. A Shopify accountant focuses on ecommerce businesses and typically has experience with:

• Shopify Payments payouts and payout reporting (what’s in a payout, what’s netted, and why bank deposits don’t match gross sales)
• Reconciling other payment gateways, such as PayPal, Sezzle, Klarna, etc.
• Ecommerce bookkeeping tools and integrations like A2X, QuickBooks Online, and Xero
• Sales tax rules for direct-to-consumer brands (plus marketplace facilitator treatment, where applicable)
• International selling complexity, including multi-currency and duties

Teresa Slack (The E-Commerce Training Academy) provides a specific example of how a specialist Shopify accountant can help you understand your margins:

When determining your selling price for your products, be sure to include not only the cost of the product but the cost to package and ship the product to you or your warehouse so it can be sold. Don’t forget any other related costs such as your packaging, product info inserts or labour to package and prep your product for sale. Understanding your true costs can ensure you set a profitable selling price – and a specialist Shopify accountant can help you with this.

Key financial challenges for Shopify businesses

1. Bulk payouts: Shopify payouts include multiple sales, fees, refunds, and taxes, making reconciliation complex.
2. Payment gateways: Each payment processor (e.g., PayPal, Stripe) has its own fees that must be properly accounted for.
3. Sales tax compliance: Shopify sellers are responsible for collecting and remitting sales tax, which can be complicated.
4. High order volume data: Large transaction volumes can slow down bookkeeping software if not managed correctly.
5. International sales: Selling globally introduces foreign exchange complexities and compliance with VAT/GST regulations.
6. Digital expenses: Ecommerce businesses have unique expenses like Shopify subscription fees, online advertising, and fulfillment costs that impact profitability.

When should you hire a Shopify accountant

Here are some common considerations that signal you should hire a Shopify accountant (or Shopify-focused bookkeeper).

1) Your payouts are hard to reconcile

• Your bank deposits don’t match your Shopify sales totals
• You have frequent refunds, chargebacks, or partial refunds
• You use multiple payment methods (Shopify Payments plus PayPal, Klarna, Afterpay, Stripe, etc.)
• You regularly “plug” reconciliation differences to make month-end work

2) Sales tax is becoming a risk, not a task

• You’ve triggered sales tax nexus in more than one state or province
• You sell into multiple countries and need VAT/GST guidance
• You’re not confident your tax settings match what you’re actually obligated to collect
• You need a repeatable process for filing, remittance, and audit-ready records

3) Your month-end close is slow or inconsistent

• You can’t close the books within 10–15 days of month-end
• Reports change each time you run them because processes are not standardized
• You’re behind on bookkeeping and making decisions on outdated numbers
• You dread month-end because it turns into a cleanup project

4) Inventory and COGS are muddy

• You don’t trust your gross margin because COGS is incomplete or inconsistent
• You use a 3PL or multiple warehouses and inventory numbers don’t tie out
• You’re running bundles, subscriptions, or preorders and don’t know how to account for them cleanly
• You’re expanding to wholesale or retail and need clearer inventory costing

5) Your business is getting more complex

• You’re selling across channels (Shopify and Amazon, Etsy, POS, wholesale, etc.)
• You’ve added multiple storefronts, currencies, or markets
• You’ve started offering B2B pricing, discounts, or more advanced promotions
• You’re planning a big operational change (new 3PL, new returns tool, new subscription app)

6) You want decision-ready financials, not just compliance

• You need reliable cash flow forecasting to plan inventory buys and ad spend
• You want to know contribution margin (after shipping, fulfillment, and ad spend), not just revenue
• You’re asking questions like “Which products are actually profitable?” and don’t have confident answers
• You want a monthly reporting cadence with clear KPIs

7) The cost of mistakes is rising

• You’ve had bookkeeping errors that impacted tax filings or cash flow
• You’ve paid penalties, missed filings, or had chargeback-related surprises
• You’ve had to restate prior months because your setup couldn’t handle volume or complexity
• You’re preparing for financing, a sale, or investor due diligence

8) You’re spending too much time in the books

• You’re doing bookkeeping at night or on weekends
• You’re the only person who understands the numbers
• You’re stuck maintaining spreadsheets instead of building systems
• You keep postponing financial work because it’s time-consuming and stressful

How to find the right Shopify accountant

Look for a partner who can clearly explain how they handle:

• Payout reconciliation for Shopify Payments and any payment gateways you use (including refunds, disputes, and fees)
• Ecommerce accounting systems: A2X + QuickBooks Online or Xero
• Sales tax
• Inventory and COGS
• Advisory support: cash flow forecasting, margin analysis, and channel profitability

Where to find a Shopify accountant

1. A2X Directory – A vetted network of ecommerce accountants.
2. Networking – Ask other Shopify sellers for recommendations.
3. Social media & online listings – LinkedIn, X (Twitter), and Reddit ecommerce communities.

Ready to find the right accountant for your Shopify store?

Search the A2X Directory now and connect with an expert ecommerce accountant today!