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Xero bookkeeping for online stores

Each of your Shopify payouts bundles many orders, takes out fees and refunds, and reaches the bank as a lump sum. We take those payouts apart in your Xero file, record the stock you buy as inventory items and keep any other channels separate, so each part of the business can be judged separately.

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  • By Book Keeping Pros
  • Sources checked 15 Oct 2026

What we keep current for an online store

The work starts with your Shopify payouts and runs through to the stock, freight and packaging bills behind each sale.

  • Your Shopify payouts matched to the orders and refunds they cover, with fees booked only as each payout's details confirm them
  • Chargebacks and disputed payments recorded against the original order, and kept on a list until each dispute is settled
  • Stock bought from suppliers entered as tracked inventory items, so each purchase is recorded against the product it was for
  • Freight and courier charges on stock deliveries recorded from the invoices, with their treatment as stock costs or expenses following your accountant's instructions
  • Sales from other channels, such as markets or wholesale customers, kept apart from the online store with tracking categories
  • Packaging, postage and fulfilment bills entered and matched to the payments that clear them
  • The store's bank and card accounts reconciled to their statements each month, with anything left unexplained listed for you

Not included

Running the store itself, such as product listings, discounts and the stock levels customers see. We keep the records in Xero from your payout, order and supplier documents.

Businesses in Non-Store Retailing (ANZSIC class 4310)

Actively trading businesses across Australia
24,869 businessesAustralian Bureau of Statistics, Counts of Australian Businesses, June 2025, checked 15 October 2026
Of those, classified as non-employing
17,968 businessesAustralian Bureau of Statistics, Counts of Australian Businesses, June 2025, checked 15 October 2026
Of those, with 1 to 4 employees
5,330 businessesAustralian Bureau of Statistics, Counts of Australian Businesses, June 2025, checked 15 October 2026

Businesses by main state or territory

These counts are for the ANZSIC class Non-Store Retailing, which covers businesses retailing goods without a shopfront or physical store. It includes internet-only retailers, mail-order sellers and other non-store sellers. Retailers with a physical shop are counted in other retail classes, even when they also sell online, so these figures are not a count of all online retailers.

  1. New South Wales8,863 businesses
  2. Victoria6,612 businesses
  3. Queensland5,290 businesses
  4. Western Australia2,029 businesses
  5. South Australia1,266 businesses
  6. Tasmania307 businesses
  7. Australian Capital Territory285 businesses
  8. Northern Territory95 businesses
Source: Australian Bureau of Statistics, June 2025. Counts of Australian Businesses, data cube 2: Businesses by main state by industry class by employment size ranges (8165DC02.xlsx). Checked 15 Oct 2026.

Businesses by number of employees

  1. Non-employing17,968 businesses
  2. 1 to 4 employees5,330 businesses
  3. 5 to 19 employees1,298 businesses
  4. 20 to 199 employees258 businesses
  5. 200 or more employees15 businesses
Source: Australian Bureau of Statistics, June 2025. Counts of Australian Businesses, data cube 2: Businesses by main state by industry class by employment size ranges (8165DC02.xlsx). Checked 15 Oct 2026.

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Online store questions about Xero

Why don't my bank deposits match my store's sales?
Because each of your Shopify payouts is a group of sales with fees and refunds already taken out. We match every payout to the orders and refunds it covers and record the fees its details show, so sales, fees and refunds each appear on their own line in Xero.
Can Xero keep track of my stock?
Xero's tracked inventory items record the quantity and cost of what you buy, and reduce the quantity when sales are recorded against them. We enter stock from supplier bills this way. How store sales should reduce those quantities is worth agreeing with your accountant before we start.
I also sell at markets and to other shops. Can those sales stay separate?
Yes. With a tracking category for sales channel, every sale and cost can be marked online, markets or wholesale, giving a profit and loss you can read channel by channel.
Will you need access to my online store?
Not necessarily. The payout and order reports from your store are enough. You can export them for us, or give us reports-only access if your store's user settings allow it.
How are disputed card payments handled?
Once a payout shows the disputed amount taken out, we record it against the original order and keep it listed until the dispute closes, whichever way it goes.

Sources

  1. Counts of Australian Businesses, data cube 2: Businesses by main state by industry class by employment size ranges (8165DC02.xlsx)

    Australian Bureau of Statistics. Actively trading businesses at 30 June 2025, released 16 December 2025. Checked 15 October 2026.

    Source: Australian Bureau of Statistics, Counts of Australian Businesses, including Entries and Exits, June 2021 to June 2025, licensed under CC BY 4.0 Licence: CC BY 4.0.

  2. Correspondence, GCCSA 2021 to GCCSA 2026 (CG_GCCSA_2021_GCCSA_2026.csv)

    Australian Bureau of Statistics. ASGS Edition 4, July 2026 to June 2031, released 22 July 2026. Checked 15 October 2026.

    Source: Australian Bureau of Statistics, Australian Statistical Geography Standard (ASGS) Edition 4, licensed under CC BY 4.0 Licence: CC BY 4.0.