Key takeaways
What this article covers, in order:
- The transactions an online store gets wrong
- 6 options for ecommerce accounting
- What to look for in ecommerce accounting software
- The chart of accounts an online store needs
- How to choose, in order
- Frequently asked questions
A marketplace pays you a fortnightly lump that is sales minus commission minus advertising minus refunds minus a reserve. One deposit, six different ledger entries. Book it as revenue and every margin number you have is wrong.
That is the question this page answers: which accounting software holds an online store's transactions properly, and what to check before you commit.
The transactions an online store gets wrong
Before the software list, the accounting. These are the entries this vertical books incorrectly most often, and the correct treatment — if a package cannot do these cleanly, nothing else about it matters.
A marketplace payout. Split it: gross sales, commission, advertising, refunds, reserve movement. One revenue line understates sales and hides every fee you pay.
Inbound freight and duty. Part of landed cost in inventory, not a period expense. Expensed, gross margin looks better than it is on every unit.
A customer return. Reverse the sale and put the stock back at cost — and only if it is resaleable. Netting refunds against sales loses the return rate, which is the number that tells you the listing is wrong.
6 options for ecommerce accounting
| Option | What it is known for | Typically suits |
|---|---|---|
| HelloBooks | Cloud ledger with AI-assisted bookkeeping and bank feeds | Businesses wanting AI-assisted bookkeeping, with a free plan to start on |
| Xero | Cloud ledger with bank feeds and a wide add-on ecosystem | Businesses whose accountant already works in Xero |
| QuickBooks Online | General-purpose small-business ledger with a large app marketplace | Businesses that want the widest choice of third-party add-ons |
| Zoho Books | Ledger inside the wider Zoho business suite | Teams already running other Zoho products |
| FreshBooks | Invoicing-led bookkeeping aimed at service businesses | Service businesses that bill by project or by the hour |
| Sage Business Cloud | Long-established accounting line with cloud editions | Businesses wanting a long-established vendor with local support |
Positioning, not pricing. Published prices and plan contents change too often for a table to stay true, and the tier carrying the one feature you need is usually not the entry tier — so take the current figure from each vendor's own pricing page before you shortlist. Fit for ecommerce is settled by the criteria below, against your own numbers.
What to look for in ecommerce accounting software
Generic accounting checklists are the reason this decision goes wrong. These are the 7 criteria that actually separate the options for an online store:
- Marketplace settlement broken into gross sales, fees, advertising, refunds and reserves
- Landed cost per SKU, including freight and duty, not just the supplier invoice
- Sales tax or VAT by destination, including marketplace-facilitator rules
- Refunds, chargebacks and returned stock put back at the right value
- Multi-channel inventory across your own site and each marketplace
- Multi-currency with the gain or loss separated from the margin
- Cost of goods sold at the point of sale, so margin is per order and not monthly guesswork
The chart of accounts an online store needs
Whatever you choose, set it up with these accounts rather than the default template. The codes are illustrative; the separations are the point.
1200 Inventory at landed cost
1210 Inventory in transit
1220 Stock held at fulfilment centres
1130 Marketplace settlement receivable
4000 Online sales — gross
4100 Refunds and returns — contra
5000 Cost of goods sold
6400 Marketplace commission and advertisingHow to choose, in order
- Write down the three entries above as they happen in your business, with real figures from last month.
- Put each shortlisted package through all of them in a trial. Not a demo — a trial, with your own numbers.
- Check the reports you will actually be asked for: ecommerce profitability, and whatever your tax authority expects.
- Only then compare price, and compare the tier that includes what you needed in step 2.
Frequently asked questions
What is the best accounting software for ecommerce?
There is no single best one; there is a best one for a shape of business. For an online store, work down the criteria in the section above and stop at the first option that clears all of them — that list is short, usually two or three.
The criteria that eliminate most options fastest are: Marketplace settlement broken into gross sales, fees, advertising, refunds and reserves; Landed cost per SKU, including freight and duty, not just the supplier invoice; Sales tax or VAT by destination, including marketplace-facilitator rules.
Give me a list of accounting software for ecommerce that offer the best security?
Ask for evidence rather than adjectives. The things worth checking, in order: an independent audit you can see (SOC 2 Type II or ISO 27001, with the report date), encryption in transit and at rest, enforced multi-factor authentication, role-based permissions fine enough that a bookkeeper cannot export your whole ledger, an immutable audit trail of who changed what, where your data is hosted and under which country's law, and a stated backup and recovery position.
Then ask the question the brochure will not answer: can you see, after the fact, who changed a figure and what it was before? For an online store that audit trail is worth more than any single feature on the security page. A vendor who will send the audit report under NDA is telling you something; one who answers with the words "bank-grade security" is telling you something too.
Is there free accounting software for ecommerce?
There are free tiers, and they are real — but the limit is what matters, not the price. Find the cap before you move your books: how many documents or transactions a month, how many bank accounts, how many users, and whether the free tier includes the one thing you came for. HelloBooks has a free plan; /pricing lists what it covers today.
How much does accounting software for ecommerce cost?
Published prices move, and the figure that matters is the one including the module you actually need — inventory, payroll or multi-currency are often a tier up, so the headline price is rarely the price you pay. Price each shortlisted option at the tier that carries what you actually need, on the vendor's own page, on the day you decide.
How do I switch accounting software without losing my history?
Migrate on a period boundary and bring three things: opening trial balance, open customer and supplier balances, and your chart of accounts. Transaction history can usually stay in the old system as a read-only archive — attempting to re-import years of detail is where most migrations lose a week and a reconciliation.
Where to go next
- HelloBooks for ecommerce
- HelloBooks in the United States
- HelloBooks pricing and what each plan includes
This guide is written for businesses in the US, UK, Canada, Australia, New Zealand and Singapore. Tax treatment differs by country — check the rule for yours before you act on it.
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