QuickBooks vs FreshBooks vs Wave: Best Accounting Software for Shopify, Etsy, Amazon Sellers
For your Shopify, Etsy, or Amazon store, accurate accounting isn't just a good idea — it's key to knowing if you're actually making money. Between platform fees, shipping costs, and tracking inventory across multiple channels, it's easy to lose track. QuickBooks, FreshBooks, and Wave each fit different types of online sellers. Picking the right one now avoids a messy migration and big headaches when tax season hits.
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The quick answer
Use QuickBooks if you have inventory, sell on multiple platforms like Shopify and Amazon, or plan to grow and hire. It’s built for tracking Cost of Goods Sold (COGS) and connecting with bookkeepers familiar with e-commerce. Choose FreshBooks if you sell custom-made items on Etsy or offer e-commerce consulting services, where detailed invoicing and project tracking matter more than inventory. Go with Wave if you're just starting, like a Facebook Marketplace seller turning legit or a new Etsy shop, and need free tools to track sales and expenses without a budget.
Side-by-side breakdown
QuickBooks Online is the go-to for serious online sellers. It connects with inventory apps, tracks sales from Shopify, Amazon, or Etsy, and helps you manage your Cost of Goods Sold (COGS). It makes sense of your platform fees (like Shopify transaction fees or Amazon FBA fees) and shipping costs. Most e-commerce accountants prefer it. Starts around $30/month.
FreshBooks is great if your "e-commerce" involves custom design work, digital products that need specific project billing, or if you consult for other online sellers. Its invoicing is top-notch for charging clients for a custom Etsy order or your consulting time, letting you see profit per project. It doesn't handle physical product inventory well. Starts around $17/month.
Wave is free accounting software for very small online businesses. Perfect for tracking income from a few Etsy sales or Facebook Marketplace flips. It handles basic sales, returns, and business expenses (like packaging or shipping labels). Payroll for one person and payment processing are extra, but the core accounting is free. It's simple but lacks deeper e-commerce integrations or robust inventory features.
When to choose QuickBooks
Pick QuickBooks when your online store gets serious. This means you’re tracking inventory across multiple channels like your Shopify store and Amazon FBA, or you need to manage sales tax collected in different states. If you're buying materials, assembling products, and need to know your true Cost of Goods Sold (COGS) for each item, QuickBooks handles that. It’s also essential if you hire virtual assistants, warehouse staff, or an e-commerce bookkeeper, as most professionals use it to manage things like Amazon FBA fees, Etsy transaction costs, and shipping expenses.
When to choose FreshBooks
FreshBooks is best for specific niches within online selling. If you sell custom digital products, unique made-to-order crafts on Etsy, or offer e-commerce consulting services (like setting up Shopify stores for others), FreshBooks shines. It’s ideal for billing clients by project or hour for a custom design or marketing package. You can quickly see if that big custom order was truly profitable, tracking your time and materials without getting bogged down by physical inventory management across platforms.
When to choose Wave
Wave is your free starting line if you’re just dipping your toes into online selling. Think first-time Etsy sellers, trying out a few products on Facebook Marketplace, or a pre-launch Shopify store. You need to track simple income from sales and basic expenses (like shipping labels, packaging, or listing fees) without paying a monthly software fee. It’s good for solo ventures with minimal inventory. As soon as you add employees, carry significant stock, or need detailed sales tax reporting for multiple states, start planning your move to a more robust system.
The verdict
For growing online stores with inventory, multiple sales channels, or staff: QuickBooks. For custom-made products, digital services, or e-commerce consulting: FreshBooks. For new Etsy shops, Facebook Marketplace sellers, or pre-revenue ventures needing basic tracking: Wave. Most serious online sellers will eventually need QuickBooks as their business scales, especially when dealing with complex inventory or sales tax. It's always easier to switch before you have hundreds of transactions.
How to get started
Start with Wave if your online store is brand new or still in the testing phase, especially before you hit consistent sales. Plan to move to QuickBooks (or FreshBooks for service-focused e-commerce) before you hire your first assistant, start managing significant inventory, or sell on more than one major platform. Connect your dedicated business bank account and credit cards immediately. Reconcile your transactions monthly to catch any missing Shopify payouts, Amazon fees, or Etsy refunds. Your first time filing sales tax and income tax will quickly reveal if your current accounting system is actually working for your online business.
RECOMMENDED TOOLS
QuickBooks Online
The industry-standard small business accounting platform
FreshBooks
Invoicing and project profitability for service businesses
Wave
Free double-entry accounting for small businesses
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FREQUENTLY ASKED QUESTIONS
Can I use Wave and then switch to QuickBooks?
Yes, but the migration requires exporting data and re-entering or importing into QuickBooks. Do it before your first tax year ends so you have clean records. Many bookkeepers charge a fixed fee to handle the migration.
Do I need a bookkeeper if I use accounting software?
Accounting software records transactions. A bookkeeper reconciles, categorizes, and ensures the records are accurate. For businesses with significant revenue, a part-time bookkeeper saves more than their cost in avoided errors and tax savings.
What is the difference between accounting software and invoicing software?
Invoicing software creates and tracks invoices but does not do double-entry bookkeeping. Accounting software maintains a general ledger, income statement, and balance sheet. You need accounting software, not just invoicing, for tax compliance.
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