Xero vs QuickBooks for Shopify Stores: Which is Right for You?

Running a Shopify store sounds exciting orders coming in, products going out, and money rolling in. But let’s face it, behind every thriving ecommerce business is a solid accounting setup. That’s where things can get confusing, especially when deciding between two big names: Xero vs QuickBooks for Shopify.

Both are powerful accounting tools. But which one is better for your Shopify store? Let’s cut through the noise and give you a clear, detailed breakdown so you can make the right decision.

Why Your Choice of Accounting Software Matters

qBefore we get into features, let’s quickly talk about why this decision matters so much. As a Shopify seller, your income and expenses are constantly moving. You deal with customer orders, shipping fees, inventory costs, taxes, and possibly refunds sometimes all in one day.

Using the wrong accounting software can lead to:

• Incorrect tax filings
  
• Confusing or missing reports
  
• Wasted time on manual data entry
  
• Messy books that make it hard to grow
  

Choosing the best accounting software for Shopify helps you stay on top of everything from sales taxes to cash flow without needing to be an accountant yourself.

Feature-by-Feature Comparison

Let’s start by breaking down the key features that Shopify store owners care about. We’ll keep it practical and easy to understand.

1. Invoicing and Billing

• QuickBooks:
  
  • Allows you to create detailed, customized invoices.
    
  • Add your logo, set payment terms, and send recurring invoices.
    
  • Useful if you also sell B2B or offer wholesale pricing.
    
  • You can send automated reminders for overdue invoices.
    
• Xero:
  
  • Has clean, modern invoice templates.
    
  • Offers options for one-time and recurring invoices.
    
  • Lets you accept online payments via Stripe, PayPal, and others.
    
  • Reminders and tracking are easy to manage.
    

Hook: If you hate chasing clients for payments, both tools make that job easier but QuickBooks offers more flexibility.

Verdict: Go with QuickBooks if you need more custom invoice options. Xero works best if you’re focused on DTC and want something clean and straightforward.

2. Reporting & Dashboards

• QuickBooks:
  
  • Very powerful here. You get access to 80+ built-in reports depending on your plan.
    
  • Create profit and loss reports, cash flow summaries, and track expenses by category.
    
  • Highly customizable you can build your own reports or modify existing ones.
    
• Xero:
  
  • Comes with essential reports like P&L, balance sheet, and cash flow.
    
  • Dashboard shows bank balances, invoices owed, bills to pay, and more.
    
  • Reports are more visual, so beginners find it less overwhelming.
    

Hook: Want to know where your money is going without hiring a bookkeeper? Your reporting tool is your best friend.

Verdict: If you love data and want to dig deep, QuickBooks gives you more options. If you prefer visuals and simplicity, Xero keeps things clear.

3. Multi-Currency Support

If you sell internationally, multi-currency support is a must.

• QuickBooks:
  
  • Available only on the Advanced plan (around $200/month).
    
  • Once enabled, you can send invoices, record expenses, and track income in foreign currencies.
    
  • Includes real-time exchange rate updates.
    
• Xero:
  
  • Offered in their Established Plan ($65/month).
    
  • Handles multiple currencies well especially helpful for global sellers.
    
  • Automatic exchange rate updates via XE.com.
    

Verdict: Xero’s multi-currency support is easier to set up and manage. Plus, it’s cheaper than QuickBooks for this feature.

Pricing Differences (With Real Numbers)

Pricing matters, especially when you’re just starting your ecommerce journey. Here’s a clearer view of what you’ll pay (U.S. pricing may vary by country):

QuickBooks Online

• Simple Start – $30/month
  
• Essentials – $60/month
  
• Plus – $90/month
  
• Advanced – $200/month

Xero

• Early – $15/month
  
• Growing – $42/month
  
• Established – $65/month
  

Hook: You don’t want to overpay for features you’re not using. That’s money better spent on ads or stock.

Verdict: Xero is more affordable for startups. QuickBooks becomes more useful as your business scales.

Integration with Shopify (And How They Actually Work)

Getting Shopify to talk to your accounting software isn’t always easy. Let’s look at the reality.

QuickBooks Shopify Integration

• Requires third-party apps like QuickBooks Connector, OneSaas, or Bold Commerce.
  
• Users often report sync delays or miscategorized transactions.
  
• You may need manual review for payout breakdowns (Shopify takes a fee from each transaction).
  

Xero Shopify Integration

• Works smoothly with tools like A2X, Link My Books, and Xero’s native connector.
  
• Automatically imports Shopify sales, refunds, taxes, shipping, and fees.
  
• Easy reconciliation with Shopify Payments and PayPal.
  

Hook: Imagine finishing your books in 10 minutes instead of hours. That’s what good integration should feel like.

Verdict: Xero wins big here. Most Shopify-specific apps are built with Xero in mind first.

Bank Feeds and Reconciliation

• QuickBooks: Connects with all major banks. Uses AI to categorize transactions. Offers rules for repeated expenses.
  
• Xero: Also connects with major banks. Very beginner-friendly reconciliation. You can split transactions and match payouts to orders easily.
  

Verdict: Both tools do this well, but Xero’s interface is simpler for people who aren’t finance pros.

Inventory Tracking

• QuickBooks Plus/Advanced: Includes built-in inventory management. Tracks cost of goods sold (COGS), stock levels, and reorder points.
  
• Xero: Basic inventory tracking is available, but for more features you’ll need apps like DEAR Systems, Cin7, or TradeGecko/QuickBooks Commerce.
  

Verdict: QuickBooks offers better inventory tools out-of-the-box. Xero depends on third-party apps for advanced inventory.

Limitations to Consider

• QuickBooks:
  
  • Higher pricing for essential ecommerce features
    
  • Shopify integrations aren’t as strong or consistent
    
• Xero:
  
  • Lacks built-in inventory management for scaling brands
    
  • Fewer trained accountants in some regions
    

User Scenarios – What’s Best for Different Shopify Sellers?

1. The Side Hustler (Under $5,000/month)

Best Option: Xero affordable, simple, and enough for your needs.

2. Growing Brand ($5k–$50k/month)

Best Option: Start with Xero + A2X or Link My Books. Switch to QuickBooks later if needed.

3. Established Store ($50k+/month)

Best Option: QuickBooks Advanced full control, reporting, multi-user access, inventory tools.

What If You Switch Tools Later?

Many Shopify sellers start with Xero and later move to QuickBooks as the business grows. Migration is possible, but it takes proper planning to avoid losing transaction history. Tools like Jet Convert and Mover.io can help migrate data accurately. Or you can hire professionals (like us!) to ensure a safe transfer.

Final Comparison Table

FAQs

Q: Can I use both Xero and QuickBooks together?
A: Technically no. You should only use one tool at a time to avoid duplication and confusion.

Q: What’s the best tool for UK Shopify sellers?
A: Xero is very popular in the UK ecommerce space because of its clean VAT support and strong Shopify integrations.

Q: What if I use Amazon or Etsy too?
A: Both Xero and QuickBooks can handle multi-channel selling, but you’ll need tools like A2X or Link My Books to consolidate data properly.

How eSeller Accountant Can Help

At eSeller Accountant, we don’t just set up your accounting tools—we make sure they work for you. Whether you choose Xero or QuickBooks, we’ll:

• Integrate it with your Shopify store
  
• Set up your reporting dashboards
  
• Help you understand your real profits
  
• Handle your monthly bookkeeping and taxes
  

Let’s talk. Book your free consultation today and get expert advice on the best fit for your Shopify store.

You’ve worked hard to grow your store. Let’s make sure your books are growing with it.