The Complete Guide To Online Invoice Payment Processing

Many small businesses — maybe even your own — use Square for its free POS app and easy-to-use card readers. Since its launch, Square has become known as a payment processor. In 2014, the company also added Square Invoices, a solution that allows businesses to invoice and accept payments with ease.

If you’re already signed up with Square, the Invoices feature is part of your Dashboard. If you don’t have an account, you can sign up at no cost and take advantage of Square’s great features, including Square Invoices.

With Square Invoices, you can send automatic payment reminders or schedule recurring payments quickly and easily. You can also add attachments and a spot for tips to your invoices. Once you’ve customized your invoices, you can send them for free. However, payment processing comes at a cost (which we’ll discuss in just a moment). Square Invoices also works with Square Installments, so you can offer payment plans to your customers without the hassle of integrating additional products.

Square Invoices has a well-designed UI and is easy to use once you grasp everything Square offers. Square Invoices users like the ease of use, mobility, and customizability of invoices, but there have been complaints surrounding the costly transaction fees and a lack of invoice templates.

Square Invoices Pricing

There are no monthly fees to use Square Invoices. Sending invoices is free. Accepting payments by cash or check is also free. However, if you want to accept online payments, you will pay 2.9% + $0.30 per invoice.

Pricing for Square products and services can get complicated. Check out our Square pricing guide, where we break down Square’s costs and fees.

Choose Square Invoices If…

FreshBooks has become the accounting and invoicing software for over 10 million businesses. For an additional fee, you can also add FreshBooks Payments — an online payment gateway and virtual terminal that allows you to accept payments online, in-person, or over the phone.

FreshBooks Payments integrates with your FreshBooks accounting software, allowing you to add an online payment option to your invoices easily. Payments are automatically recorded to your FreshBooks account, so there’s no more worrying about reconciliation. You’ll also be able to take advantage of features such as recurring invoices and other automations. FreshBooks Payments also doesn’t require a separate merchant services account.

Setting up an account is easy, and there are no monthly fees to use FreshBooks Payments. There are no hidden costs, so all pricing is transparent and easy to understand. FreshBooks is also known for its award-winning customer service and has an overall excellent reputation with its clients.

FreshBooks Payments Pricing

You won’t pay any monthly fees or hidden charges with FreshBooks Payments. For credit or Apple Pay transactions, you will pay 2.9% + $0.30 per transaction. For ACH payments, you’ll pay a 1.0% bank transfer fee.

If you’re new to FreshBooks, take a look at our FreshBooks pricing guide to fully understand the cost of using FreshBooks accounting software and FreshBooks Payments.

Choose FreshBooks Payments If…

Does your business use QuickBooks as its accounting solution? If so, you don’t have to look very far to find a payment processor when you take advantage of QuickBooks Payments (also known as Intuit Merchant Services).

QuickBooks Payments is a merchant services provider that uses Fiserv as its back-end payment processor. There are four different products to choose from based on what version of QuickBooks you use: QuickBooks Online Payments, QuickBooks Desktop Payments, QuickBooks GoPayment, and QuickBooks Point of Sale.

QuickBooks Payments has a lot of benefits, especially if you’re already using the software. You can easily add a “Pay Now” button to your invoices, receive your funds the next day or instantly, and send reminders to your customers. You’ll even get real-time alerts when your customers open or pay their invoices. The biggest draw for many users is that QuickBooks Payments seamlessly integrates with QuickBooks. Payments are automatically reconciled to invoices, helping you keep your books balanced.

QuickBooks Payments has solid customer service and a good reputation among its users. However, some users have reported long waiting times when contacting customer support, while others have complained about the lack of invoice customization options.

QuickBooks Payments Pricing

The pricing structure for QuickBooks can get a little complicated, as it’s based on the product you’re using and whether you choose a monthly plan or the pay-as-you-go option.

QuickBooks Online Payments has no monthly fee and does not charge for ACH transfers. Charges for other transactions are:

• Swiped Credit/Debit: 2.4% + $0.25 per transaction
• Invoices/ApplePay/PayPal: 2.9% + $0.25 per transaction
• Keyed Transactions: 3.4% + $0.25 per transaction

With QuickBooks Desktop Payments, you have two options: pay-as-you-go and a pay-monthly plan. The pay-as-you-go plan has no monthly fee. Other fees include:

• ACH Transfer: $1/each
• Swiped Credit/Debit: 2.4% + $0.30 per transaction
• Invoices/Apple Pay: 3.5% + $0.30 per transaction
• Keyed Transactions: 3.5% + $0.30 per transaction

With the monthly plan, you’ll pay a monthly fee but save on your transaction fees. If you sign up for QuickBooks Desktop Payments monthly plan, these are the fees you should expect:

• Monthly Fee: $20
• ACH Transfer: $1
• Swiped Credit/Debit: 1.6% + $0.30 per transaction
• Invoices/Apple Pay: 3.3% + $0.30 per transaction
• Keyed Transactions: 3.3% + $0.30 per transaction

If you use the QuickBooks POS system, you’ll want to check out QuickBooks POS Payments. There are two plans to choose from: Basic and Pro.

The Basic Plan has no monthly fee. Other fees for this plan are as follows:

• Swiped Credit/Debit: 2.7%
• PIN Debit: 1.0%
• Keyed Transactions: 3.4%

The Pro Plan has a monthly fee. Transaction fee rates are slightly lower, but there is a per-transaction fee, so keep this in mind and run a few calculations to check which is the better value for your business.

• Monthly Fee: $19.95
• Swiped Credit/Debit: 2.3% + $0.25 per transaction
• PIN Debit: 1.0% + $0.25 per transaction
• Keyed Transactions: 3.2% + $0.25 per transaction

For mobile processing, you might want to consider GoPayment. This solution has no monthly fee. You will, however, have to pay for the following:

• Swiped Transactions: 2.4%+ $0.30 per transaction
• Keyed Transactions: 3.4%+ $0.30 per transaction

For all plans, PCI compliance is an opt-in service priced at $9.95/month for pay-as-you-go customers. Pricing for pay-monthly customers is as much as $100/year. Additional fees to be aware of when using QuickBooks Payments include:

• Returned Check Fee: $10
• ACH Rejection Fee: $25
• Chargeback Fee: $25

Want to know more about QuickBooks Pricing? Get the details by checking out our guide on QuickBooks Desktop pricing. If you’re a QuickBooks Online user, our post on QuickBooks pricing and costs can help you easily tally up potential fees.

Choose QuickBooks Payments If…

If you’re looking for an all-in-one solution that’s easy to set up and use for accepting online payments, look no further — PayPal may be the right choice for your business.

One of the benefits of PayPal is that you’ll be working with a company that has a trusted name among consumers and merchants. This third-party payment processor offers a variety of additional features and benefits for merchants, including customizable invoices with no monthly fees, mass payouts, and the PayPal Here mobile processing app.

You can send invoices and receive online payments exclusively using PayPal’s business products and services, or you can use a PayPal integration with your existing third-party solutions.

PayPal offers solid customer service and tech support and is viewed favorably by most users. However, high transaction fees, account holds, and chargebacks are common complaints about using PayPal. This product is best for low-volume businesses or micro-merchants.

PayPal Pricing

If you are a PayPal Standard or Pro user, transaction fees are as follows:

• Online Transactions: 2.9% + $0.30 per transaction
• Swiped In-Store Transactions: 2.7%
• Keyed-In Mobile & In-Store Transactions: 3.5% + $0.15
• Virtual Terminal Transactions: 3.1% + $0.30 per transaction
• Mass Payouts: 2% using the online form ($1 maximum) or $0.25 per payout using the API

Additional fees worth noting include:

• Chargebacks: $20
• Transactions Originating Outside Of The US: 1.5% fee
• Instant Transfer Fee: 1% of the transfer amount (with a maximum fee of $10)
• Micropayment Processing: 5% + $0.05
• PayPal Payments Pro: $30/month

Choose PayPal If…

Stripe is a payment service that combines third-party payment processing with a payment gateway. Stripe counts businesses such as Lyft, Pinterest, and Under Armour among its clients, and it’s easy to see why. Stripe isn’t just your typical payments service; it offers a variety of developer features that make it an ideal choice for online businesses, especially SaaS businesses or any business that accepts recurring payments.

With Stripe, you can accept more than 135 currencies. Businesses can accept payments online, in person, or via mobile apps by using this service. Stripe also has a comprehensive set of developer tools for quick and easy integration.

You have the option to use a Stripe plugin or integrate the payment service via one of its integration partnerships. You can use Stripe with your existing invoicing solution or send invoices through Stripe Billing.

If you encounter any issues, you can get in touch with Stripe 24/7 through its phone and chat support. Stripe has a pretty good reputation among merchants. However, there are a few complaints, most notably about the lack of fraud protection, account holds, and terminations. One last thing to keep in mind is that this service can be difficult to use, as it was built with developers in mind. Less-experienced users may want to test out other options on the market (and on this list) before using Stripe.

Stripe Pricing

Stripe is transparent about its pricing and charges a flat rate of 2.9% + $0.30 for credit card transactions and 0.8% (capped at $5) for ACH transactions.

There are a few additional costs to be aware of. Stripe Billing offers two plans — Starter and Scale. The Starter plan is free for the first $1 million in transactions. After this, a flat rate of 0.4% (plus processing fees as listed above) is charged per transaction. The Scale plan costs 0.7% (plus processing fees) per transaction.

Stripe Terminal is available for a cost of 2.7% + $0.05 per transaction. Merchants can also purchase one of two card readers for an additional fee.

Stripe charges additional fees for other services, including the Sigma advanced reporting tool and Radar advanced fraud tools.

Want to learn more about pricing? Take a look at our guide to Stripe pricing and costs for more details.

Choose Stripe If…

Authorize.Net is a payment processor that has provided services to over 400,000 merchants since it first launched in 1996. Before we go into what Authorize.Net is, let’s first look at what it isn’t. It is not a merchant account provider. While a merchant account option is available, pricing is steep, so we recommend using one of the following merchant account options with Authorize.Net instead: Payment Depot, CDGcommerce, and Payment Cloud.

What Authorize.Net does well is offer payment processing services that integrate with numerous third-party shopping carts. You’ll also receive free virtual POS software (with a card reader available for a fee), a free mobile POS app (again, a card reader is available for an additional fee), the Customer Information Manager that allows you to store customer data securely, and Automated Recurring Billing.

Authorize.Net supports numerous payment methods, including credit cards, debit cards, Apple Pay, Chase Pay, Visa Checkout, and echecks.

You’ll also have access to excellent customer support, transparent pricing and sales, and no hidden fees. While Authorize.Net has a pretty good public reputation, there have been some user complaints regarding data portability and billing issues.

Authorize.Net Pricing

There are two pricing plans to consider when signing up for Authorize.Net’s services. The first plan is for the payment gateway only. Fees for this plan are:

• Gateway Fee: $25/month
• Processing Fee: $0.10 per transaction
• Daily Batch Fee: $0.10

If you want a payment gateway plus a merchant account, you’ll pay the following fees:

• Gateway Fee: $25/month
• Processing Fee: 2.9% + $0.30 per transaction processing fee

Additional fees to note include:

• International Transaction Fee: 1.5%
• eCheck Processing: 0.75% per transaction
• Chargebacks: $25

Choose Authorize.Net If…

Braintree Payment Solutions allows businesses to accept online invoice payments with secure bank-sponsored merchant accounts combined with a payment gateway. Rates are fair and transparent, and there are no surcharges or fees.

Braintree stands out for its support of numerous payment methods, including debit, credit, ACH Direct Debit, Android, Apple Pay, Venmo, Google Pay, PayPal, MasterPass, and Visa Checkout. Braintree also offers international processing and allows you to accept payments in over 130 currencies. Add in solid customer support and an excellent public reputation, and you’ll quickly see why we’ve given Braintree a 5-star review.

While Braintree has received favorable reviews, some customers have complained about account setup times and insufficient fraud protection. Braintree’s services are also not suited for high-risk businesses.

Braintree Payment Solutions Pricing

Braintree offers simple, easy-to-understand pricing, which is refreshing compared to some of the more complicated pricing structures you’ll find among merchant account providers. Rates are 2.9% + $0.30 per transaction for domestic transactions. International transactions come with a 1% fee, and payments made on cards issued outside the US are also charged a 1% fee.

For ACH Direct Debit, fees are 0.75% per transaction, with a maximum charge of $5. Volume discounts, nonprofit discounts, and custom pricing are also available.

Choose Braintree Payment Solutions If…

If you primarily sell your products and services to other companies and you’re ready to take the leap into online invoice payments, Dharma Merchant Services may be a good option for your business. This merchant account provider stands out for its fair pricing, transparency, and exceptional customer service.

Dharma has a vast selection of products and services to help your business tackle accepting online invoice payments. This includes B2B processing, the MX Merchant virtual terminal and invoicing system, and MX Merchant Express mobile processing. If you need a payment gateway, Dharma has you covered by offering the choice between Authorize.Net and NMI Gateway.

Other benefits of Dharma include no contracts, early termination, PCI compliance fees, or batch fees. This certified green business has an outstanding reputation among its customers and consistently provides solid customer support, transparent pricing, and the products you need to run your business more efficiently.

Dharma Merchant Services Pricing

Dharma offers four rate plans based on different business categories.

The Storefront Plan is ideal for retail businesses. Costs for this service are as follows:

• Monthly Fee: $25
• Merchant Rates: Interchange + 0.15% + $0.08 per transaction (interchange + 0.25% + $0.08 per Amex transaction)

eCommerce businesses can take advantage of Dharma’s Virtual rates, which are:

• Monthly Fee: $25
• Merchant Rates: Interchange + 0.20% + $0.11 per transaction (interchange + 0.30% + $0.11 per Amex transaction)

Dharma also has a plan for restaurant owners. Those rates are:

• Monthly Fee: $25
• Merchant Rates: Interchange + 0.15% + $0.08 per transaction (interchange + 0.25% + $0.08 per Amex transaction)

Finally, Dharma offers a high-volume retail rate plan. For this plan, you’ll pay:

• Monthly Fee: $20
• Merchant Rates: Interchange + 0.10% + $0.08 per transaction card-present transaction (interchange + 0.20% + $0.08 per Amex card-present transaction)

There are additional fees to be aware of if you choose Dharma as your merchant services provider. These include incidental fees of $20 for chargebacks and $5 for retrieval fees. If you also plan to use one of Dharma’s payment gateways, there is an additional charge of $10/month and $0.05 per transaction.

Dharma also has a B2B program that offers discounts on processing charges. This service requires the MX B2B app that’s priced at $20/month.

Choose Dharma Merchant Services If…

If you’re in an industry such as retail, eCommerce, or wholesaling, CDGcommerce may be the right solution for you. CDGcommerce is a merchant services provider that offers many great features at competitive pricing with no hidden fees.

What stands out about CDGcommerce? It’s worth noting that its customer service and top-quality products have allowed this company to hold a 97% customer retention rate. Other notable features include a free payment processor, multiple pricing options, processing for high-risk businesses, and a free virtual terminal. You can also add on mobile payments, credit card terminals, or a traditional POS system at competitive prices.

CDGcommerce also offers exceptional customer support, including 24/7 phone support. Its public reputation is excellent, with very few negative customer reviews.

CDGcommerce Pricing

There are several different pricing plans for CDGcommerce’s merchant account services, so consider the needs of your business when determining which plan to choose.

The flat-rate pricing plan is ideal for businesses that process less than $10,000 per month. The pricing under this plan is as follows:

• Swiped Or Mobile (Card-Present) Transactions: 2.75% + $0.30 per transaction
• Keyed Transactions: 2.75% + $0.30 per transaction + 0.15% surcharge
• Online Transactions: 2.90% + $0.30 per transaction
• ACH Debit Transactions: 0.75% + $0.15 per transaction

The interchange-plus plan may be the best option for you if you process more than $10,000 and up to $200,000 each month. Fees for this plan are:

• Swiped Transactions: Interchange + 0.25% + $0.10 per transaction
• Online/Keyed Transactions: Interchange + 0.30% + $0.15 per transaction
• ACH Debit Transactions: 0.75% + $0.15 per transaction
• Monthly Fee: $19-$49/month

Finally, CDGcommerce offers a subscription plan based on the amount you process each month. Those plans are priced as follows:

• Up To $75,000/Month: $79/month with a flat rate of interchange + $0.10 per transaction
• Up To $200,000/Month: $99/month with a flat rate of interchange + $0.07 per transaction
• $200,000+/Month: $149/month with a flat rate of interchange + $0.06 per transaction

Additional fees to note include $25 chargeback fees, $15 retrieval fees, and $0.25 batch fees.

Choose CDGcommerce If…

Fattmerchant has offered payment processing services since 2014, and the company also provides invoicing through its Virtual Terminal product. You can also add on other Fattmerchant services (such as mobile payments, a physical terminal, and an online shopping cart) since they are all compatible to create your personalized payment solution.

Fattmerchant Virtual Terminal offers a decent amount of features and is easy to use. It also offers a unique pricing structure, which we’ll look at in detail in just a moment. Where Fattmerchant stands out, though, is its customer support, which customers frequently praise. Fattmerchant offers 24/7 phone and email support and a variety of other resources to help you get the most out of the service.

On the downside, though, Fattmerchant Virtual Terminal can be expensive for businesses with low processing volumes. Limited customization options for invoices and missing features that you’d find with other invoicing software could prove to be dealbreakers for some businesses.

Fattmerchant Virtual Terminal Pricing

There are two different plans you can select: Fattmerchant Starter Platform and Fattmerchant Enterprise Platform.

The Starter Platform is available for $99/month. You’ll also pay $0.15/per transaction + direct cost interchange fees for payment processing. With this plan, you’ll get access to features, including invoicing, inventory, and integration with QuickBooks Online.

The Enterprise Platform is priced at $199/month. You’ll also pay $0.15/per transaction + direct cost interchange fees. This plan includes everything from the Starter Plan plus additional features, such as reporting, priority risk monitoring, chargeback monitoring, and a dedicated customer success manager.

Add-ons, including same-day funding, terminal protection plan, analytic reporting, and advanced invoice customization, are available for additional fees.

Choose Fattmerchant Virtual Terminal If…