Pharmacies

Tax Accountant for Pharmacists in Ontario

Helping Independent Pharmacies Stay Compliant, Profitable & Tax-Efficient

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AFFORDABLE Accountant for Pharmacists & Pharmacies

Operating a pharmacy means running a complex business with strict financial and regulatory responsibilities. From inventory management and POS transactions to payroll, HST filings, and CRA compliance, pharmacists need an accountant who understands the pharmacy industry, not just general bookkeeping. Working with an experienced accountant for pharmacists ensures your financial records are accurate, compliant, and aligned with your business goals.

At Gondaliya CPA, we provide specialized tax services for pharmacies designed to support independent pharmacists and multi-location pharmacy owners. Our accounting solutions cover bookkeeping, payroll, inventory tracking, corporate tax planning, and year-round CRA compliance. Whether you operate a single pharmacy or manage multiple locations, we help you reduce tax exposure, improve cash flow, and make informed decisions that support long-term growth and stability.

Official Partner

Accounting That Understands Pharmacy Operations

Pharmacies operate in a highly complex financial environment with fast-moving inventory, multiple revenue streams, and tight margins. Between tracking cost of goods sold, managing expiry and shrink, reconciling third-party insurance payments, and applying the correct HST treatment, pharmacists need more than basic bookkeeping. Our accounting services are built specifically for pharmacy operations, helping owners maintain accurate records, stay CRA-compliant, reduce tax exposure, and clearly understand profitability across prescriptions and front-store sales.

Inventory and COGS Tracking

Accurate tracking of purchases, expiry, and shrink to protect pharmacy margins.

Insurance and Vendor Reconciliation

Clear reconciliation of insurer receivables and supplier accounts.

HST on Prescriptions and Retail Sales

Correct tax treatment to avoid CRA issues and missed credits.

CRA/HST Audit Risk

Stay compliant and avoid CRA audit headaches with professional guidance.

Stay Compliant with Pharmacy Tax Rules

HST on Pharmacy Sales

Pharmacies deal with a mix of taxable front-store items and zero-rated prescriptions and professional services. Proper sales coding and accurate HST filing are essential to avoid CRA reassessments, penalties, or missed input tax credits.

Payroll, Records, and CRA Expectations

Managing payroll for pharmacists, technicians, and assistants requires accurate remittances, time tracking, and source deductions. Clean inventory records, daily sales reports, and organized documentation help keep your pharmacy audit-ready.

Corporate Tax and Owner Compensation

Most pharmacies operate through corporations and require accurate T2 filings and year-end financial statements. Strategic salary and dividend planning helps pharmacy owners manage personal tax, support financing needs, and prepare for expansion or sale.

Why Choose Our Accounting Services for Pharmacists?

Industry-Focused Expertise

We understand the unique structure of pharmacy businesses—drug margins, third-party billing, wholesaler rebates, and inventory-heavy models. Our pharmacy CPAs build systems that simplify it all.

Bookkeeping Designed for Pharmacies

We manage your daily sales, vendor payables, and expense tracking—integrated with your POS and supplier systems for smooth reporting.

Strategic Tax Planning for Pharmacy Owners

Whether you’re incorporated or planning to be, we help reduce tax through deferrals, income splitting, eligible deductions, and retirement-focused strategies.

CRA Compliance & Peace of Mind

From HST filings to pharmacy-specific tax audits, we ensure your records are accurate, reconciled, and fully compliant with Canadian tax laws.

Why Work with Gondaliya CPA?

Pharmacy-Focused Expertise

We understand pharmacy operations, inventory, reimbursements, and CRA requirements.

Clear, Actionable Reporting

Know your real profit with clean financials built for decision-making.

Tax-Smart Planning

Reduce tax legally with proactive corporate and personal tax strategies.

Year-Round Support

Not just at tax time—we stay available as your pharmacy grows.

Fully Licensed CPA Ontario

500+ ★★★★★ Google Reviews

30-Day Money-Back Guarantee

60-Day Fees-Matching Policy

Pharmacy Accounting and Tax Services

Corporate Tax Filing for Pharmacies

Professional Corporate tax preparation and return filing, ensuring accuracy and CRA compliance.

Accounting & Bookkeeping for Pharmacies

Reliable bookkeeping and accounting with financial statements, records, and reporting.

Corporate Tax Planning for Pharmacies

Smart Corporate tax planning to optimize savings, reduce liabilities, and maintain compliance.

CPA Compilation Report (Notice to Reader) for Pharmacies

Deliver clear CPA Compilation Reports (Notice to Reader) for reliable financial insights.

Trust and Estate Tax Returns (T3) for Pharmacies

Expert preparation of T3 returns to ensure compliance and minimize taxes for trusts and estates.

Corporate Tax Cleanup for Pharmacies

Resolve past corporate tax issues and bring your filings fully compliant and up to date.

CRA Audit Resolution Services for Pharmacies

Expert support to handle Canada Revenue Agency audits, disputes, and negotiations with confidence.

Resident Director (Nominee Director) Services for Pharmacies

Provide qualified Nominee Director and Resident Director services to help companies meet compliance requirements.

Incorporation Services for Pharmacies

Incorporation services for smooth business formation, entity setup, and start-up support.

Free Resource: 50 Deductible Expenses for Pharmacies

Comprehensive checklist of tax-deductible costs unique to Pharmacies. PDF delivered instantly.

Case Studies

Independent Pharmacy in Mississauga

Problem: Inventory purchases, expiry losses, and shrink were not being tracked properly, making COGS unreliable and margins unclear.

Solution: We implemented accurate inventory valuation, expiry tracking, and monthly financial reporting tailored to pharmacy operations.

Result: Improved gross margins, fewer write-offs, and clear insight into true profitability month over month.

Multi-Location Pharmacy Owner in Toronto

Problem: HST treatment varied between stores, and financial reporting was inconsistent across locations, increasing CRA risk.

Solution: We standardized HST coding, reconciled insurance receivables, and introduced consolidated multi-store reporting.

Result: Clean CRA-ready compliance and clear performance comparisons across all pharmacy locations.

Pharmacist-Owner in Brampton

Problem: High personal tax exposure with no clear plan around incorporation or owner compensation.

Solution: We structured the pharmacy corporation properly and created a tax-efficient salary and dividend strategy.

Result: Reduced overall tax burden, predictable cash flow, and a long-term plan for growth or future sale.

How We Work: Your Year-End Flow

Step 1

Initial Consultation

We start with a no-pressure conversation to understand your pharmacy’s business structure, software systems, and immediate financial needs.

Step 2

Tailored Tax & Accounting Plan

We create a custom plan based on your ownership structure—independent, incorporated, or partnership—with a focus on cash flow, tax minimization, and real-time visibility.

Step 3

Execution, Reporting & Support

We handle your monthly bookkeeping, payroll, HST remittances, and year-end corporate tax returns—so you can stay focused on serving patients.

Step 4

Continued Partnership

Offering ongoing support to adapt to changes and drive sustained success.

Get Your Pharmacy Tax-Ready Today

Transparent Pricing for Pharmacies

Pricing

We believe in clear, upfront pricing so you know exactly what to expect.

- Tax Preparation (Corporation): From $400
- Tax Return Filing (Corporation): From $400
- Tax Compliance Audit – FREE CRA audit support for our clients
- Tax Strategy: FREE for our clients
- Accounting Base Plan – From $100 / month
- Bookkeeping Management (Free for our Accounting clients)
- Financial Reporting (Free for our Accounting clients)
- Business Formation: Flat $35
- Incorporation Process: Flat $35
- Entity Setup Assistance: Flat $35
- Full-Service Payroll: From $125 per month

Meet Your Lead Pharmacy Tax Accountants

Sharad Gondaliya, CPA

Principal 📞 647-212-9559 sharad@gondaliyacpa.ca

Vandana Goel, CPA

Accounting Specialist 📞 647-250-0242 vandana@gondaliyacpa.ca

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We manage day-to-day bookkeeping, track expenses, and provide clear financial reports so pharmacy owners can focus on operations.

Why do pharmacies need specialized accounting?

Pharmacies face unique challenges such as insurance reimbursements, inventory management, strict regulations, and complex tax rules. Specialized accounting helps ensure compliance, manage cash flow, and optimize taxes so pharmacy owners can focus on patient care and business growth.

Can you prepare and file taxes for pharmacies?

Absolutely — we handle tax preparation and filing for both incorporated pharmacies and self-employed pharmacy owners.

How does your tax planning benefit pharmacy owners?

We develop proactive strategies to minimize taxes, optimize deductions, and keep your pharmacy compliant with CRA regulations.

Do you manage payroll for pharmacy staff?

Yes — we handle payroll processing, source deductions, remittances, and ensure compliance so your staff is paid accurately and on time.

Can you help me incorporate my pharmacy business?

Yes — we guide you through the incorporation process, set up accounting systems, and ensure CRA registrations are in place.

Do you provide ongoing advisory support for pharmacy businesses?

Through our CFO and tax planning services, we provide ongoing financial guidance tailored to pharmacy owners.

Do you offer cloud-based bookkeeping solutions for pharmacies?

We implement and manage secure, modern accounting software to make your pharmacy’s finances more efficient.

Do you help pharmacies plan for growth or expansion?

Yes — through our CFO and tax planning services, we provide financial forecasting, budgeting, and strategy guidance to help pharmacy owners successfully expand or open new locations.

How do I get started with accounting services?

The first step is a consultation with our corporate accountant.
Contact Gondaliya CPA today to discuss your accounting needs and receive tailored solutions for Toronto, Ontario, or anywhere in Canada.