
Payment Processing for Accountants and Accounting Firms
An accounting firm can finish a tax return on time and still spend weeks collecting the fee. A client forgets a cheque, an invoice gets

Many merchants unknowingly pay more than necessary in payment processing. This overpayment impacts a business’s profitability and growth.
This article covers the reasons for overpayment, including hidden fees, pricing models, merchant account setup, lack of transparency, and practical steps merchants can take to reduce these costs.
The payment processing value chain has multiple participants and steps, including the merchant, the customer, the acquiring bank, the issuing bank, and the payment processor. Each entity requires compensation for their role, resulting in a complex fee structure. The primary fees include:
These fees vary based on the type of card used (debit, credit, rewards), the transaction size, and the merchant’s industry.
A big reason merchants overpay is due to hidden fees and surcharges that aren’t immediately obvious. Payment processors often advertise low rates, but these rates may only apply to specific types of transactions or under certain conditions. Common hidden fees include:
These hidden fees can quickly accumulate, significantly increasing the overall cost of payment processing for merchants.
The pricing model chosen by a merchant greatly influences their payment processing costs. The three primary pricing models are:
Merchants often overpay because they are placed on pricing models that are not optimal for their transaction profile. For example, a merchant with primarily low-risk transactions may overpay on a flat-rate model.
Setting up a merchant account correctly is important for businesses to avoid unnecessary fees and optimize their payment processing costs. An incorrect setup leads to higher fees, impacting the overall profitability of a business. Here are some common setup mistakes:
Many merchants end up paying higher fees because they do not negotiate effectively with payment processors. This lack of negotiation generally happens because of a lack of knowledge about the industry, an underestimation of their bargaining power, or simply accepting the first offer presented by the processor. Payment processing fees are not set in stone and often have room for negotiation, especially for businesses with high transaction volumes or a strong credit history.
Without proper negotiation, merchants may miss out on lower rates, better terms, or waived fees that could significantly reduce their overall processing costs. For instance, merchants might agree to standard rates without questioning or understanding the potential for lower interchange rates, volume-based discounts, or reduced chargeback fees.
Selecting the right payment processor has a big difference on minimizing payment processing fees. Merchants who choose a processor that is not well-suited to their business size or transaction volume often incur higher fees.
For smaller merchants, especially those with annual transaction volumes below $200,000, using a payment aggregator like Square, PayPal, or Stripe can be cost-effective. Aggregators offer simplicity and convenience, as they provide an all-in-one solution with straightforward pricing structures and no long-term contracts. They typically charge a flat rate per transaction, which can be beneficial for businesses with low or inconsistent sales volumes.
However, as the business grows, these flat-rate fees can become disproportionately high compared to the more customized pricing models available through dedicated merchant accounts.
Larger merchants with annual transaction volumes exceeding $200,000 should consider obtaining a dedicated merchant account, such as those offered by Clearly Payments. Dedicated merchant accounts provide more tailored solutions, including lower interchange rates and the ability to negotiate fees based on transaction volume and risk profile.
Dedicated merchant accounts often come with additional benefits such as enhanced customer support, more robust fraud prevention tools, and greater flexibility in terms of payment options and integrations.
Another major factor contributing to overpayment is the lack of transparency in the payment processing industry. Many processors do not fully disclose their fee structures, making it challenging for merchants to compare options and understand their costs.
Additionally, merchants often lack the education needed to navigate the complexities of payment processing. Without a clear understanding of how fees are structured and what options are available, merchants are at a disadvantage when negotiating with processors.
To avoid overpaying for payment processing, merchants can take several proactive steps:

An accounting firm can finish a tax return on time and still spend weeks collecting the fee. A client forgets a cheque, an invoice gets

Credit card payments typically take 1–3 business days to settle, although some transactions can settle as quickly as the next business day. The exact timing

Businesses in the United States and Canada have hundreds of payment processing providers to choose from, including merchant account providers, acquiring banks, payment facilitators, ISOs,