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QuickBooks bookkeeping for pharmacies

A pharmacy is a dispensary and a shop under the same roof, each with its own sales system, its own suppliers and its own margins. In QuickBooks, we keep both sides clear, from wholesaler statements and credits to the takings that reach the bank.

  • By Book Keeping Pros
  • Sources checked 15 Oct 2026

Bookkeeping across the dispensary and the shop

Much of a pharmacy's stock comes in on wholesaler accounts, and its takings come out of separate dispensing and point of sale systems. The work is keeping supplier balances right and each side's sales distinct.

  • Dispensary takings and point of sale takings each entered from their own end-of-day figures, then matched to what reached the bank through card settlements and cash banking
  • Dispensary and shop sales and costs kept under separate classes on a QuickBooks plan with class tracking, giving each side its own profit figure
  • Wholesaler invoices entered as deliveries arrive and checked against each wholesaler statement before it is paid, picking up missing invoices and duplicates
  • Credit notes for returned, damaged or out-of-date lines applied to the wholesaler's account, so the amount paid reflects the credits the pharmacy is owed
  • Money paid by payers other than the customer at the counter traced to the reports your dispensing system produces, with short or unexplained amounts listed for your follow-up
  • Front-of-shop supplier accounts for cosmetics, vitamins, fragrance and gift lines kept separate from the wholesaler, with a list of unpaid supplier bills showing what is due to whom
  • Card terminal settlements reconciled against merchant statements, with terminal charges booked from the statement and any shortfall it doesn't explain flagged

Not included

Work inside the dispensing and point of sale systems, such as pricing and stocktakes. We record the takings, payments and supplier bills those systems produce.

Businesses in Pharmaceutical, Cosmetic and Toiletry Goods Retailing (ANZSIC class 4271)

Actively trading businesses across Australia
8,990 businessesAustralian Bureau of Statistics, Counts of Australian Businesses, June 2025, checked 15 October 2026
Of those, classified as non-employing
2,818 businessesAustralian Bureau of Statistics, Counts of Australian Businesses, June 2025, checked 15 October 2026
Of those, with 1 to 4 employees
1,702 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 Pharmaceutical, Cosmetic and Toiletry Goods Retailing, which includes cosmetic and toiletry retailers as well as pharmacies, so they describe a wider group than pharmacies alone.

  1. New South Wales3,102 businesses
  2. Victoria2,128 businesses
  3. Queensland1,830 businesses
  4. Western Australia965 businesses
  5. South Australia641 businesses
  6. Tasmania174 businesses
  7. Australian Capital Territory110 businesses
  8. Northern Territory33 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. 5 to 19 employees3,188 businesses
  2. Non-employing2,818 businesses
  3. 1 to 4 employees1,702 businesses
  4. 20 to 199 employees1,266 businesses
  5. 200 or more employees16 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.

Pharmacy owners' questions about QuickBooks

Can the dispensary and the shop be reported separately?
On a QuickBooks plan with class tracking, yes. The dispensary and the shop each become a class, sales and costs are recorded against the right side, and reports by class compare their results. Without classes, this class-based breakdown is unavailable; we can agree another reporting approach with your accountant.
Should we track stock in QuickBooks as well as in our point of sale?
That depends on where your stock is counted now. QuickBooks plans that include inventory can hold quantities on hand and flag lines that are running low, but where your point of sale already counts stock item by item, a second count adds work. Either way, the stock value in the accounts follows the figures and method your accountant provides.
Our wholesaler statement doesn't agree with QuickBooks. Can you find out why?
We check every line of the statement against the wholesaler's account in QuickBooks and note what causes each difference, for example a missing invoice, a credit still to be applied or a delivery billed in duplicate. Differences the paperwork can't account for are returned to you so the wholesaler can be asked.
We take wholesaler deliveries most days. How do the invoices reach you?
Whichever way suits the pharmacy: invoices emailed by the wholesaler, a shared folder, or copies sent with the statement. We enter them against the wholesaler's account as they arrive, then check the total against the statement before payment.
Can you match the payments we receive for prescriptions?
Yes. Each payment that reaches the bank is matched to the report your dispensing system produces for it. If an amount is short or doesn't line up with a report, we list it for your dispensary team to look into.

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.

  3. Get started with class tracking in QuickBooks Online (Australia)

    Intuit Australia Pty Ltd. Current at 16 October 2026, released 16 October 2026. Checked 16 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).

  4. Set up and track your inventory in QuickBooks Online (Australia)

    Intuit Australia Pty Ltd. Current at 16 October 2026, released 16 October 2026. Checked 16 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).

  5. Reconcile an account in QuickBooks Online (Australia)

    Intuit Australia Pty Ltd. Current at 16 October 2026, released 16 October 2026. Checked 16 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).