Best Bookkeeping Software for a New Online Store (2026)

Bookkeeping software records what your store earns and spends, categorizes payouts, and keeps clean reports for tax time. A new shop can track initial sales in a spreadsheet, but software saves time once transactions multiply and tax deadlines approach.

Below, we compare QuickBooks Online, Xero, and Wave using official US list prices and plan limits checked on 2026-10-03. The worked example below shows the true software cost for a new store at 30 and 300 orders a month.

The three tools in one table

Worked example: monthly bookkeeping costs at 30 and 300 orders

To see what software actually adds to your overhead, consider two realistic ecommerce stores. Both sell a physical product at an average order value of $40 with a unit cost of $12 and shipping of $6. Orders come through an online checkout where the store platform and card processor charge standard rates.

Because regular checkout orders are processed on your website, your online storefront handles consumer transactions. Bookkeeping software sits behind the scenes: it imports your bank deposits and records payouts, supplier bills, and expenses.

Store A: a new side-business shipping 30 orders a month ($1,200 in gross sales)

Store A takes 30 orders a month. The founder pays $360 for products (30 × $12), $180 for shipping labels (30 × $6), and roughly $43.80 in card processing fees (assuming a standard 2.9% + 30¢ rate: 2.9% of $1,200 = $34.80, plus 30 × 30¢ = $9.00). That leaves $616.20 in operating margin before software subscriptions.

Here is what the three software options cost Store A per month, and the net profit remaining:

At 30 orders a month, bookkeeping fees on QuickBooks Simple Start take $38 out of $616.20—more than 6% of your remaining margin. Wave Starter costs $0, keeping your overhead at zero. Xero Early costs $27 a month and easily fits your order volume because 30 ecommerce orders synced from your bank count as zero direct invoices.

Store B: a growing brand shipping 300 orders a month ($12,000 in gross sales)

Store B does 10 times the volume: 300 orders at $40 for $12,000 in gross revenue. Product costs total $3,600 (300 × $12), shipping costs total $1,800 (300 × $6), and card fees total $438 (2.9% of $12,000 = $348, plus 300 × 30¢ = $90). Operating profit before accounting software is $6,162.

Store B also receives 8 wholesale supplier invoices a month for raw materials, boxes, and freight.

Because Store B processes 8 supplier bills a month, Xero Early (limited to 5 bills) no longer fits. Store B must choose Xero Growing at $59 a month. On QuickBooks, Simple Start ($38) still works if only one person logs in. If an assistant and an outside bookkeeper both need access, QuickBooks Essentials at $85 a month covers 3 users.

Wave Starter still costs $0, because its free tier includes unlimited bills and bookkeeping records.

Rule of thumb for bookkeeping software

• Under 50 orders a month ($2,000 sales): stick to Wave Starter ($0) or a spreadsheet. Paying $38 to $85 a month for accounting software burns 5% to 15% of your net profits before your store has steady traction.
• Between 50 and 300 orders a month: if you need automated sales tax summaries or bank reconciliation rules, Xero Early ($27/mo) or QuickBooks Simple Start ($38/mo) costs between 0.5% and 2% of gross sales.
• Run it with your own numbers: subtract your software subscription and bank fees from your store margin: Gross Sales - Product Cost - Shipping - Card Fees - Bookkeeping Plan = Net Profit. Use the profit per order calculator to test single-order margins, and check our monthly cost guide to map your full budget.

Wave: best for keeping monthly software overhead at zero

Wave is the only major provider here with a permanent free plan. Its Starter plan costs $0 and includes unlimited estimates, invoices, bills, and bookkeeping records.

What Wave includes

• Unlimited records: create unlimited bookkeeping entries and track income and expenses without paying a monthly base fee.
• Bank connections via Plaid: if your financial institution supports Plaid connections, Wave imports transactions automatically into your ledger.
• Invoicing and bill management: send unlimited invoices and track supplier bills.
• Optional merchant payments: if you invoice clients directly, Wave offers credit card processing at 2.9% + $0.60 per transaction (3.4% + $0.60 for American Express).
• Pro upgrade: Wave Pro costs $19 a month billed monthly, which lowers transaction fees on Wave payments to 2.9% + $0.
• Advisors packages: for owners who want help with reconciliation, Wave Advisors packages start at $149 a month.

When Wave is not for you

• You require built-in inventory tracking: Wave does not list inventory tracking features on its pricing plans. Read our inventory basics guide for how to track SKUs outside your accounting ledger.
• Your bank does not connect with Plaid: automatic imports rely on Plaid, so an unsupported bank means entering statements manually or via CSV.

Xero: best for structured sales tax tracking and reconciliation

Xero offers a clear three-tier plan ladder: Early ($27/month), Growing ($59/month), and Established ($97/month). Each plan offers a promotional discount for the first 3 months.

What Xero includes

• Core features on Early: the $27 entry plan includes bank reconciliation, sales tax tracking, W-9 and 1099 management, and quotes.
• Strict entry limits: the Early plan restricts you to 20 invoices and 5 bills per month.
• Uncapped growing tier: the Growing plan ($59/month) removes the limits on invoices and bills.
• Inventory add-on: Xero lists Inventory Plus as an optional add-on for stores that manage product stock.

When Xero is not for you

• You manage high bill volumes on a shoestring: if you enter more than 5 supplier bills each month, Early will force an upgrade to Growing ($59/month).
• You want a zero-cost option: Xero does not have a permanent free tier.

QuickBooks Online: best for multi-user teams and deep plan tiers

QuickBooks Online is the industry standard for US accountants. Its pricing ladder spans four tiers: Simple Start ($38/month for 1 user), Essentials ($85/month for 3 users), Plus ($140/month for 5 users), and Advanced ($340/month for 25 users). The pricing page features a 30-day free trial or a 50% discount for the first 3 months, with no annual contract and cancel-anytime terms.

What QuickBooks includes

• Automated bank matching: QuickBooks automatically matches and records bank transactions as it learns your financial activity.
• Integrated payments: invoices can accept credit cards and bank transfers through QuickBooks Payments.
• Sales Tax AI: QuickBooks lists a Sales Tax AI feature designed to catch discrepancies before filing.
• Enterprise inventory: the top-tier Advanced plan ($340/month) lists built-in tools for tracking and managing inventory.

When QuickBooks is not for you

• You want a cheap entry price: Simple Start is $38 a month, making it the most expensive entry plan compared here.
• You need inventory tracking on a starter budget: inventory management is listed on the Advanced plan ($340/month), which is far beyond the budget of a new store. If you manage variable products, tracking SKUs inside Shopify or WooCommerce avoids this cost.
• You have more than one user on a budget: adding a second user requires jumping from Simple Start ($38) to Essentials ($85).

Sales tax: what bookkeeping software does not do

All three platforms offer features to record sales tax on orders and invoices. QuickBooks features Sales Tax AI, and Xero includes sales tax tracking on its Early plan.

However, accounting software does not automatically register your business or file state tax returns. As Shopify notes in its tax documentation: “It’s important to consult a tax professional for questions and setups unique to your business, and to ensure you file and remit your taxes correctly.”

For details on establishing tax nexus and managing permits, read our business basics guide and our review of sales tax software for online stores.

Common mistakes when setting up store bookkeeping

1. Mixing personal and business funds. The single biggest bookkeeping headache is paying for supplier goods or shipping labels with a personal debit card. Open a dedicated business checking account on day one before launching your store, as outlined in how to open an online store.
2. Paying for advanced accounting inventory too soon. Advanced software plans that track inventory cost hundreds of dollars a month (such as QuickBooks Advanced at $340/month). Most ecommerce platforms like Shopify and WooCommerce already track product SKUs, inventory adjustments, and stock levels at no extra charge.
3. Ignoring transaction and bill limits. Picking Xero Early saves money upfront ($27/mo), but if you receive 10 supplier invoices and wholesale bills a month, you will exceed its 5-bill cap and need the $59 Growing plan.
4. Budgeting around 3-month promotional prices. Both QuickBooks (50% off 3 months) and Xero offer promotional pricing. Budget your operating expenses using the full list price ($38/mo or $27/mo) so your profits do not take a surprise hit in month four.
5. Treating software as a replacement for tax advice. While tools calculate totals and flag errors, you are legally responsible for filing accurate local, state, and federal tax returns.

How to decide what to do this week

1. Open a dedicated business bank account. Keep every order payout, shipping expense, and supplier charge completely isolated from personal funds.
2. Calculate your monthly bill volume. If you sell through a website and receive fewer than 5 supplier bills a month, you can use any tool. If you receive more than 5 bills, avoid Xero Early or budget $59 for Xero Growing.
3. Start with Wave Starter if you want $0 software overhead. Sign up for Wave Starter at $0, connect your business bank account through Plaid, and log in once a week to categorize payouts and expenses.
4. Choose Xero Early if you want sales tax reporting on a budget. If your business needs formal sales tax tracking and bank reconciliation for $27 a month, start with Xero Early.
5. Choose QuickBooks Online if your accountant insists on it. If you already work with a CPA who requires QuickBooks, start on Simple Start ($38/month) and test it with the 30-day free trial.

For help cutting software expenses across your whole stack, read how to cut your store app subscriptions and see our list of free tools for a new online store.

Sources (checked 2026-10-03)

• Wave: Pricing, Starter $0 plan, Pro $19 plan, credit card transaction fees, Plaid bank connections, Wave Advisors starting price
• Xero US: Pricing plans, Early $27, Growing $59, and Established $97 plans, 20-invoice and 5-bill limits, sales tax, Inventory Plus add-on
• QuickBooks Online: Pricing, Simple Start $38, Essentials $85, Plus $140, Advanced $340 plans, user limits, 30-day trial, promotion, bank matching, Sales Tax AI, inventory tracking on Advanced
• Shopify Help Center: US tax guide, guidance to consult a tax professional

General information, not legal or tax advice.