Comprehensive Guide to Payment Processing
Software in Canada for 2025

The ideal payment processing software for small businesses in Canada largely depends on your project requirements. Here are some popular options:

• Wave –  Best for very small businesses and freelancers, offering free accounting and pay-per-transaction pricing
• Square – Suitable for retail and in-person businesses, with simple flat-rate pricing
• Shopify Payments – Best for e-commerce businesses already using Shopify
• Helcim – Great for growing businesses, with interchange-plus pricing that improves with volume

It is recommended that small businesses opt for solutions with no monthly fees, a modest pricing structure, and quick setup in order to reduce overhead costs at the project outset.

If you are looking for a payment processor with the lowest rates in Canada, consider:

• Helcim – Offers interchange-plus pricing (typically interchange + 0.40% + 8¢ for in-person) that automatically gets better as your users grow
• Moneris – Canada’s largest processor, provides competitive rates for established businesses, especially those banking with RBC or BMO
• Square – While rates aren’t the absolute lowest, the processor’s 2.5% fee for in-person transactions with no monthly fees can be a cost-effective option for businesses with lower transaction volumes.

Remember, the “lowest rate” depends on your business type, transaction volume, and average transaction size. For instance, interchange-plus pricing models are best for growing businesses processing over $10,000/month, offering the best long-term value. Also, when comparing rates, always estimate the total cost of ownership, including monthly fees, PCI compliance fees, and any other add-ons when comparing rates.

To set up online payment processing for your Canadian website, follow these steps:

• Select a payment processor – Pick a provider like Stripe, PayPal, or Moneris that supports Canadian dollar transactions and supports Interac payments. 
• Set up your merchant account – Complete the application process, which usually involves submitting business documents and banking information.
• Integrate with your website – If you’re using platforms like WordPress/WooCommerce or Shopify, use plugins for easier integrations. For custom websites, you must implement the processor’s APIs.
• Configure checkout settings – Set your preferred currency (CAD), tax rates (GST/HST/PST), and shipping options.
• Test the system – Run some test transactions in sandbox mode to make sure everything works before going live. 
• Launch and monitor – After testing, switch to live mode and keep an eye on early transactions to ensure everything’s running smoothly.
• For e-commerce sites, consider choosing a solution with hosted checkout pages. This will simplify PCI compliance and reduce your security burden.

Yes, businesses can accept Interac e-Transfer payments automatically through:

• Interac e-Transfer for Business – Allows for automated deposits without security questions
• Wave Payments – Offers Interac e-Transfer processing integrated with their invoicing system
• Plooto – Provides automated Interac payments for B2B transactions
• Banking APIs – Some Canadian banks offer direct API access for automating e-Transfer receipts
  To set up automated Interac e-Transfer processing:
• Contact your bank about their “Autodeposit” or “e-Transfer for Business” features
• Register your business email or mobile number for automatic deposits
• Consider platforms like Wave or Plooto that offer integration with accounting software

Interac e-Transfer processing typically has lower fees than credit card processing, making it an attractive option for Canadian businesses.

Canadian businesses handling payment card data must adhere to:

• PCI DSS (Payment Card Industry Data Security Standard)
• PIPEDA (Personal Information Protection and Electronic Documents Act)
• EMV Compliance (chip-and-PIN transactions)
• Interac Security Requirements (for debit transactions)
  To ensure compliance:
• Use a processor offering tokenization to avoid storing card data
• Complete the appropriate PCI Self-Assessment Questionnaire (most small businesses qualify for SAQ A)
• Implement data handling procedures per PIPEDA
• Use only certified EMV-compliant terminals
• Ensure customer data is encrypted in transit and at rest

The simplest way to minimize the burden is to use hosted checkout pages or tokenization services that keep card data off your servers.

For seamless integration, consider:

• QuickBooks Payments – Native integration with QuickBooks Online
• Wave Payments – Built into Wave’s free accounting platform
• FreshBooks Payments – Fully integrated with FreshBooks
• Stripe – Integrations with QuickBooks, Xero, and Sage
• Moneris – Integration with Sage 50 and QuickBooks
• Helcim – QuickBooks and Xero integrations with automatic syncing

Key features to look for include automatic transaction syncing, proper categorization of fees and taxes, reconciliation with bank deposits, customer record syncing, and GST/HST reporting support. Integrated payment/accounting systems can save over five hours of bookkeeping per week for the average small business.

Consider these specialized processors:

• Square for Restaurants – Integrated payments, tableside ordering, and delivery management
• Clover – Versatile POS with table mapping and tip management
• TouchBistro + Moneris – Canadian-developed restaurant POS integrated with Moneris
• Lightspeed Restaurant – Advanced restaurant management with integrated payments

Essential features include table management, tip pooling/distribution, split bills, menu modifiers, tableside payments, online ordering integration, and Interac acceptance. Restaurant-specific processors typically charge 2.4–2.6% for in-person transactions and offer robust hardware for busy environments.

Yes, there are many special payment processing options for charities and non-profits. Here are a few:

• Moneris Charity Rate – Discounted rates for registered charities
• PayPal for Nonprofits – Reduced fees (1.6% + $0.30)
• Stripe for Nonprofits – Discounts and extra features for qualifying organizations
• iATS Payments – Focused on non-profits
• CanadaHelps – Donation processing platform

Important features include automated tax receipting, recurring donation management, event registration/ticketing, donor management integration, and mobile giving support. Always inquire about non-profit rates and have your CRA registration number handy when applying.

These processors are more likely to work with high-risk merchants:

• PayKings – Specializes in high-risk accounts
• Nuvei – Solutions for regulated industries
• Netpay – Works with various high-risk verticals
• Secure Global Pay – High-risk merchant services
• T1 Payments – Services for challenging industries

High-risk sectors include cannabis/CBD, online gambling, adult services, nutraceuticals, subscription services with free trials, travel agencies, and debt collection. Expect higher rates (3.5–8%), longer contracts, and reserve requirements. Partner with a processor experienced in your industry to avoid account terminations.