The best accounting and bookkeeping software for ecommerce
- Zoho Books ranks first for online sellers, with inventory from Professional.
- QuickBooks Online is second, with native Shopify, Amazon and Square connectors.
- Xero and FreshBooks reach Shopify only through partner apps.
- Puzzle ranks last and lists no store connection.
- A busy store pairs its ledger with a payout connector.
| Tool | Picked for | Type | Free plan | Starting price | Rating | Score |
|---|---|---|---|---|---|---|
| 1 Zoho Books | Owners who want a free plan for a micro business and paid plans that add inventory and multi currency. | Software | Yes | Freezoho.com/us/books/pricing | 4.4 | 71 |
| 2 QuickBooks Online | Small businesses that want full bookkeeping with four priced plans and connected store, POS and payment apps. | Software | Yes | Freequickbooks.intuit.com/pricing | 4.3 | 70 |
| 3 Xero | Owners who want bank reconciliation on every plan, with store and POS apps from partners. | Software | No | $27 a monthxero.com/us/pricing-plans | 4.1 | 47 |
| 4 FreshBooks | Service businesses that invoice clients and track time, with billing features on every plan. | Software | No | $23 a monthfreshbooks.com/pricing | 4.5 | 44 |
| 5 Puzzle | US dollar startups that want bank connected books and reconciliation on a flat monthly plan. | Software | No | $30 a monthpuzzle.io/pricing | 3.2 (1 review) | 23 |
Zoho Books ranks first among the accounting and bookkeeping software scored for online stores, because it combines native Shopify and Amazon connections with inventory at a modest price. Picking a ledger comes before picking a connector, and starting with the right ledger covers the general case. Stores that sell on Shopify then need tools that post Shopify payouts, and the two Shopify connectors compared is the closest head-to-head.
How I ranked these
Inventory and store connections tie for the top weight, followed by the price for one business and customer sentiment. Multicurrency, sales tax handling and price transparency come after. That order favors tools that track stock and connect to Shopify and Amazon natively. Open the QuickBooks Online page or the Xero page to see every level for those two. Sellers who ship to many states also meet sales tax, and if TaxJar is not the fit lists the other tax tools.
What a store needs from the ledger
A store needs the ledger to track stock, post sales and fees, and handle foreign currency when it sells abroad. Tax software for shipping to many states fills the sales tax gap that general ledgers leave. The bookkeeping side is explained in books for a Shopify or Amazon store. Sellers who also bill clients should read FreshBooks’ strengths and gaps.
Costs outside the headline price
The ledger is one cost of several. Connectors add their own monthly fee, and a second company adds a full subscription on QuickBooks Online and Xero. When the work grows past what software can carry, ecommerce-focused bookkeepers take it over for a monthly price. Each score here follows the weights behind each score.
The other side
Ranking first for ecommerce does not mean best for every seller. A service business with a small shop may prefer an invoicing-first tool, and a store with a heavy catalogue may outgrow the inventory features of every package here and need a dedicated system.
Zoho Books lists native Shopify and Amazon connections, inventory tracking from Professional at $50 a month, and multicurrency from the same plan. Sales tax tracking starts on Standard at $20. It rates 4.4 from 681 Capterra reviews. Inventory earns middling credit, and the price keeps the total on top.
- Key details
- Zoho Books
- Type
- Software
- Starting price
- Free zoho.com/us/books/pricing
- Free plan
- Yes
- Rating
- 4.4 on Capterra
Pros
- Native Shopify and Amazon connections
- Inventory and multicurrency from Professional
- Free plan for light selling
Cons
- Inventory depth earns only middling credit
- No Square connection is listed
Verdict
A well-priced ledger for a store, with inventory behind a mid-tier plan.
Inventory and multicurrency need Professional or higher, not the free or Standard plans.
Scorecard
Full scorecard
Plans and prices
QuickBooks Online lists native Shopify, Amazon and Square connectors, the strongest store-connection level here. Plus at $140 a month adds inventory and multicurrency, and Essentials at $85 adds multicurrency. A 30-day trial comes first. It rates 4.3 from 8,544 Capterra reviews. Its connectors lift it to second even though the price is higher than Zoho’s.
- Key details
- QuickBooks Online
- Type
- Software
- Starting price
- Free quickbooks.intuit.com/pricing
- Free plan
- Yes
- Rating
- 4.3 on Capterra
Pros
- Native Shopify, Amazon and Square connectors
- Inventory on Plus and Advanced
- Multicurrency from Essentials
Cons
- Inventory needs a higher-priced plan
- A second company needs a full subscription
Verdict
The most connected ledger for a multi-channel store, at a higher paid price than Zoho Books.
Inventory needs Plus or Advanced, and each additional company is a separate subscription.
Scorecard
Full scorecard
- https://quickbooks.intuit.com/online/integrations/
- https://quickbooks.intuit.com/learn-support/en-us/help-article/manage-integrations/connect-shopify-quickbooks-online/L1Xv7ZCFB_US_en_US
- https://quickbooks.intuit.com/learn-support/en-us/help-article/import-transactions/connect-amazon-seller-central-quickbooks/L7EyuwWEn_US_en_US
Plans and prices
Xero lists Shopify, Amazon, Square and Toast through partner apps, with plans at $27, $59 and $97 a month. Multiple currencies arrive on Established, and inventory is an optional add-on on Growing and Established. A 30-day trial comes first, and it rates 4.1 from 11,425 Trustpilot reviews.
- Key details
- Xero
- Type
- Software
- Starting price
- $27 a month xero.com/us/pricing-plans
- Free plan
- No
- Rating
- 4.1 on Trustpilot
Pros
- Reconciliation on every plan
- Multiple currencies on Established
- Partner apps for Shopify, Amazon and Square
Cons
- Inventory is a paid add-on
- Store connections depend on partner apps
Verdict
A solid ledger for stores that already use a connector app.
Sales tax handling earns little credit for a seller, and inventory costs extra.
Scorecard
Full scorecard
Plans and prices
FreshBooks suits a seller whose business mixes products and services. Lite is $23 a month, Plus $43 and Premium $70, with a 30-day trial. Shopify arrives through a partner app. It rates 4.5 from 4,529 Capterra reviews. Inventory earns no credit, which holds the ecommerce score down.
- Key details
- FreshBooks
- Type
- Software
- Starting price
- $23 a month freshbooks.com/pricing
- Free plan
- No
- Rating
- 4.5 on Capterra
Pros
- Top invoicing level
- Shopify through a partner app
- Rated 4.5 from 4,529 Capterra reviews
Cons
- No inventory credit
- No Amazon connection listed
Verdict
A client-billing tool first, and a thin choice for a store with stock.
Inventory and cost-of-goods tracking earn no credit.
Scorecard
Full scorecard
Plans and prices
Puzzle prices flat at $30, $72, $120 and $360 a month, with unlimited bank connections. No inventory, multicurrency, sales tax or store connection is listed, which is why it ranks last for ecommerce. Its rating is 3.2 from 1 Trustpilot review.
- Key details
- Puzzle
- Type
- Software
- Starting price
- $30 a month puzzle.io/pricing
- Free plan
- No
- Rating
- 3.2 on Trustpilot (1 review)
Pros
- Flat published prices
- Unlimited bank connections
- Reconciliation on Complete
Cons
- No store connection listed
- No inventory or multicurrency credit
Verdict
A bank-first ledger that leaves out what a store needs most.
Inventory, multicurrency and store connections earn no credit.
Scorecard
Full scorecard
Plans and prices
Common questions
What is the best accounting software for ecommerce?
Zoho Books ranks first, with native Shopify and Amazon connections and inventory from Professional. QuickBooks Online is second and has the widest set of native store connectors.
Do I need a separate connector for Shopify?
Past a handful of orders, yes. A payout connector posts fees and refunds into the ledger, and the Shopify connector page ranks the options.
Which plan tracks inventory?
Zoho Books starts inventory at Professional, $50 a month. QuickBooks Online starts it at Plus, $140 a month.
Can one subscription cover a store and a café?
Not on QuickBooks Online or Xero, which need one subscription per company. Zoho Books sets each business up as its own organization.