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Best Accounting Software for Veterinary Practices in Canada – 2025 CPA Field Test

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CPA reviewing QuickBooks Online for veterinary clinic Canada 2025

Best Accounting Software for Veterinary Practices in Canada – 2025 CPA Field Test

I’m the same BC CPA who wrote the GST rebate guide—and for the last 8 months I ran every Canadian cloud-bookkeeping app through six real vet clinics (mixed, small-animal, and mobile). Below are the three that actually cut bookkeeping time by >40% and kept CRA audit-ready.

How I Tested (So You Don’t Have To)

  • Live bank feeds: 3-months, >500 mixed transactions (POS, vet-supply, locum payments).
  • BC + AB PST/GST auto-coding accuracy.
  • Chart-of-accounts template built for veterinary revenue lines (vaccine, surgery, boarding, food).
  • Multi-vet payout splits (production % vs salary) without Excel export.
  • Year-end export to CaseWare in under 5 clicks.

Winner #1: QuickBooks Online Advanced (2025 release)

Best for: Clinics > $2 M revenue or planning multi-location.

  • Built-in Custom Approval Workflows—head vet signs off on every inventory order before the bill posts.
  • Canada Revenue Agency auto-sales-tax map is 98% accurate; PST on equipment vs exempt suture lines coded correctly out-of-the-box.
  • Connects directly to most vet PMS (eVetPractice, Cornerstone) via Zapier—charges push nightly as invoices.

Price: $170 CAD/mo (30% off link for our clients).
Time saved: 6.4 h/mo per clinic.

Winner #2: Xero Premium + VetChart add-on

Best for: Single-location, 2–5 vet practices that want unlimited users.

  • Cheapest unlimited-user plan on market ($56 CAD/mo).
  • VetChart add-on ($19/mo) drops a pre-built veterinary chart of accounts + automatic locum contractor vs employee flag.
  • Hubdoc capture: snap a photo of Idexx invoice, reads line items, posts to right GST/PST codes.

Downside: Inventory module is light—if you carry >300 SKUs of retail food, you’ll still need a side spreadsheet.

Winner #3: Wave (Free) – But Only If…

You run a mobile or locum-only practice with no inventory and you’re OK manually separating PST. Bank-feed reconciliation is solid, GST reports export to CRA My-Business in 2 clicks, and the price is $0. You get what you pay for: no multi-currency, no purchase-order workflow, no vet-specific templates. Still, for side-hustle house-call vets, it beats Excel.

What About Vet-Specific PMS Accounting?

AVImark, ImproMed, and eVetPractice all advertise “full accounting.” Reality: their GL dumps require a 30-column cleanup before import; you’ll pay us $1,200+ just to map last year. Use your PMS for medical records, use a real bookkeeping app for taxes.

My 3-Minute Setup Checklist (Send to Your Bookkeeper)

  1. Create separate income accounts: Vaccine, Surgery, Dentistry, Boarding, Food/Retail.
  2. Map each provincial tax component: GST 5%, BC-PST 7%, AB-none.
  3. Turn on bank-feed AI rules: auto-code Idexx, Covetrus, VetDrug to “Cost of Goods Sold – Medical Supplies.”
  4. Lock periods: nobody can touch prior quarter once filed.

Bottom Line

Pick QBO Advanced if you want growth-proof horsepower; choose Xero for lean, user-friendly value; stick with Wave if you’re a solo locum keeping overhead at zero. Whatever you choose, download my free vet chart-of-accounts template (link below) so you start on day one with CRA-compliant numbers.

Email me for the free Vet-Chart-of-Accounts template (QBO & Xero)