How to accept online payments for faster cash flow

Published Monday 20 April 2026

Table of contents

• Benefits of accepting online payments
• Popular online payment methods
• Choosing the right payment method for your business
• Online payment fees and costs
• How to set up online payments for your business
• Keep payments secure and prevent fraud
• Integrate payments with your accounting software
• Will online payments help you get paid faster?
• FAQs on online payments

Key takeaways

• Choose your payment method based on invoice size: use credit or debit cards for amounts under $100, switch to direct debit for larger invoices to pay a flat fee instead of a percentage, and use bank transfers for very large invoices to avoid fees entirely.
• Integrate your payment provider with your accounting software so payments and fees record automatically, saving you time on manual data entry and making bank reconciliation much simpler.
• Offer multiple payment options on your invoices, including cards and digital wallets for everyday customers and direct debit or bank transfers for business clients, so customers can pay in the way that suits them best.
• Use reputable payment providers that comply with PCI DSS standards and the ePayments Code, so you never need to store sensitive customer payment data yourself and your business stays protected from fraud.

Benefits of accepting online payments

Online payments let customers pay your invoices digitally instead of using cash or cheques, a necessary shift given the 90 per cent decline in cheque volumes over the last 10 years. They help you improve cash flow by reducing payment times from weeks to days or even minutes. The Australian Taxation Office says cash flow is the top challenge for small businesses.

Here are the key benefits for your business:

• Faster payment: Receive funds twice as fast as traditional invoicing
• Reduced admin: Spend less time chasing overdue payments
• Better cash flow: Access funds instantly for business operations

Your customers also benefit from online payments:

• Convenience: Pay invoices anytime, anywhere with one click
• Flexibility: Choose their preferred payment method
• No delays: Skip postal wait times and bank visits

Popular online payment methods

Online payment methods are digital ways customers can pay invoices without cash or cheques. With card-based payments making up about 75 per cent of non-cash retail transactions, the most popular options for small businesses include:

• Credit and debit cards: Process instant payments with 2–4% transaction fees
• Digital wallets: Use services like PayPal to process payments through customer accounts
• Direct debit: Initiate automatic bank transfers from customer accounts
• Bank transfers: Send direct account-to-account payments

These methods let your customers pay you immediately, without visiting the bank or writing cheques, which aligns with trends showing only 13 per cent of payments were made using cash in 2022.

Choosing the right payment method for your business

The best payment method depends on your transaction size, customer type and payment frequency.

Consider your typical transaction size when choosing a payment method:

• Under $100: Use credit or debit cards for convenience despite higher percentage fees
• Over $100: Use direct debit to pay flat fees instead of percentage-based charges
• Large invoices: Use bank transfers to avoid transaction fees entirely

Your customer type also influences the best payment method:

• Consumer customers: Offer cards and digital wallets for familiar checkout experiences
• Business customers: Offer direct debit or bank transfers for larger, recurring payments

Payment frequency matters when selecting your method:

• One-off payments: Use cards or bank transfers for single transactions
• Recurring payments: Use direct debit to automate collection without customer action

Most small businesses offer multiple payment options. This lets customers choose what works best for them while you optimise costs based on invoice size.

Online payment fees and costs

Online payment fees are small charges taken from each transaction to cover processing costs, and managing them is vital since small businesses on average pay twice as much to process the same transaction as large businesses. Here's what you typically pay:

Card payments using credit or debit cards have the following fee structure:

• Expect fees of 2–4% of the invoice value
• Calculate a $100 invoice as $2–$4 in fees
• Choose this method for most invoice amounts

Direct debit has a different fee structure:

• Expect fees of 20 cents to $2 per transaction
• Calculate a $1,000 invoice as $2 maximum in fees
• Choose this method for larger invoices over $100

Here are some tips to manage your payment processing costs:

• Sign up with most providers for free with no monthly fees
• Toggle payment options on or off for specific invoices
• Switch to direct debit for invoices over $100 to reduce percentage-based fees

How to set up online payments for your business

Setting up online payments connects your invoicing software to payment processors so customers can pay with one click. Most providers offer free setup with no monthly fees.

Follow these steps to set up online payments:

1. Choose a payment provider that integrates with your accounting software
2. Connect your business bank account for deposits
3. Add payment options to your invoice templates
4. Send invoices with embedded 'Pay now' buttons

Here's what happens when a customer pays your invoice:

1. The customer clicks the payment button on your invoice
2. The customer enters payment details securely
3. Funds transfer to your account minus small transaction fees
4. Payment records automatically in your accounting software

If you also sell products online, many payment providers offer website checkout options that work alongside invoice payments.

Keep payments secure and prevent fraud

Reputable payment providers use advanced security to protect your business and your customers' data from threats like payment redirection scams, which caused the highest losses to businesses in 2022. You don't need to store sensitive payment information yourself.

In Australia, these protections follow established standards:

• ePayments Code: Governs electronic payment transactions and consumer protections
• PCI DSS compliance: Ensures secure handling of card data through encryption and fraud detection

Your payment provider manages these security requirements on your behalf.

Integrate payments with your accounting software

Integrating your payment provider with accounting software automatically records payments and fees when customers pay. This saves time and reduces errors.

Integrating payments with your accounting software provides several benefits:

• Eliminate manual data entry: Payments record automatically when received
• See cash flow in real-time: Know exactly what's been paid without checking multiple systems
• Simplify bank reconciliation: Match payments to invoices with less effort
• Stay tax compliant: ATO research shows a 90% link between using accounting software and paying tax on time

Will online payments help you get paid faster?

Online payments help you get paid faster. Not every customer will pay instantly, but you will see measurable results.

Here are the typical results businesses see:

• Receive payment twice as fast on average
• Collect from 30–50% of customers immediately
• Convert late payers into on-time payers
• Predict income timing more accurately

Online payments work because they:

• Remove payment friction like cheques and bank visits
• Let customers pay when it suits them

FAQs on online payments

Here are answers to common questions about accepting online payments for your business.

How quickly will I receive payments?

Most payment providers transfer funds to your bank account within one to two business days. Some providers offer instant transfers for an additional fee.

Do I need special equipment to accept online payments?

No special equipment is needed. You only need an internet connection and accounting software that integrates with a payment provider.

Can I choose which payment methods to offer?

Yes, most payment providers let you toggle payment options on or off for each invoice. This helps you manage transaction fees based on invoice size.

Are online payments secure?

Yes, reputable payment providers use encryption and fraud detection that complies with PCI DSS standards. You don't store sensitive customer payment information yourself.

What if a customer disputes a payment?

Your payment provider handles disputes according to the ePayments Code. Contact your provider's support team if a customer raises a payment dispute.