4 Best QuickBooks Payments Alternatives for Small Businesses (2025)

QuickBooks is great at bookkeeping, but when it comes to payment processing, it’s eating into your profits. If you’re a manufacturer, wholesaler, or bookkeeper accepting large client payments, that 1% QuickBooks fee adds up fast. New accounts don’t even get a cap. A single $500,000 ACH transfer? That’s a painful $5,000 fee. 

That’s why we’re here today, to help you find the best alternative to QuickBooks Payments, so you can accept money without paying through the nose for it. 
Here’s the kicker: many businesses don’t realize they have a choice. You can skip QuickBooks Payments entirely while still using QuickBooks accounting software. Tools like Nickel offer zero-fee ACH transfers and native QuickBooks integration, giving you clean books without paying a premium to get paid. 

Margins matter, and those fees could be the difference between staying lean or bleeding cash. If you’re still paying 1% per transfer without a cap, it’s time to rethink your setup.

Key Takeaways

• QuickBooks Payments charges a flat 1% ACH fee, which adds up fast for large transactions.
• New accounts no longer have a fee cap, leading to runaway costs.
• Stripe, Square, and Melio all come with ACH fees or syncing limitations.
• Nickel offers unlimited free ACH transfers with native QuickBooks Online integration.
• Businesses can send and receive up to $1 million per transaction with no holds.
• Nickel also supports branded links, same-day ACH, and full A/R and A/P workflows.
• To keep more of your revenue, get started with Nickel for free today.

Why Small Businesses Are Ditching QuickBooks Payments

QuickBooks is great for accounting, but the moment you use QuickBooks Payments to accept ACH transfers, things get expensive fast. What was once a convenient add-on has become a major drag on profitability, especially for businesses that process large or frequent payments.

The 1% Fee Problem Just Got Worse

QuickBooks charges a flat 1% fee on ACH transfers. That alone can cost hundreds or thousands of dollars each month. The real problem? Newer accounts no longer have a fee cap. Older users had a maximum fee of $10 per transaction. That safeguard is gone.

Now, if you accept a $400,000 payment, you're handing over $4,000 in fees just for the privilege of receiving your own money.

That’s a huge hit for manufacturers, wholesale distributors, and construction suppliers who regularly deal with five- and six-figure transactions. A $250,000 invoice? That’s a $2,500 fee. Do that a few times a month, and you're giving away tens of thousands each year.

Here’s where things get really interesting, because ACH transfers only cost banks about $0.29 to process. Depending on the transaction amount, that 1% fee represents a markup of anywhere from several hundred to several thousand percent - money coming right out of your pocket. It’s both wasteful and unsustainable for small businesses operating on tight margins.

A Smarter Way to Get Paid

Depending on the payment processor, you don’t even have to ditch QuickBooks entirely. 

The accounting software is still top-tier, but platforms like Nickel offer the best of both worlds: free ACH transfers with native QuickBooks integration. That means you can manage your books exactly the way you’re used to, while cutting out the unnecessary fees.

For high-volume businesses, switching your payment processor could save $20,000 to $50,000 per year, or more, real money that actually helps your business grow. As you’ll see below, Nickel is one of the best QuickBooks Payments alternatives, although certainly not the only one. 

Top Alternatives to QuickBooks Payments in 2025

Without further ado, let’s find the top alternatives to QuickBooks Payments, starting with the number one choice, Nickel. 

1. Nickel

Nickel is the only platform built to eliminate ACH fees entirely while still working in combination with your existing QuickBooks setup. You don’t have to switch accounting software. You don’t have to sacrifice your workflows. You just stop paying ridiculous transaction fees.

Nickel gives small businesses what they actually need: unlimited, truly free ACH transfers and native QuickBooks integration that syncs payments and invoices in real time.

For manufacturers, contractors, wholesale distributors, and bookkeepers managing high-volume transactions, that means keeping thousands of dollars that would otherwise be lost to processing fees.

With Nickel, you no longer have to choose between affordable payment processing and a reliable accounting system, because you get both.

Nickel Features and Benefits

Nickel’s feature set is purpose-built for industrial and invoice-heavy businesses. Here’s what sets it apart from the competition.

Unlimited Free ACH Transfers

Nickel allows businesses to send and receive ACH payments without limits or hidden fees. You can move $10,000 or $1,000,000 and pay exactly $0 in processing charges. This is a huge bonus for anyone frustrated by QuickBooks’ 1% fee with no cap.

Native QuickBooks Integration

Nickel syncs directly with QuickBooks Online, automatically pulling in invoices and pushing back payment confirmations. No CSVs. No duplicate entry. Your accounting stays current in real time without disrupting existing workflows.

High-Value Transaction Support

Process payments up to $1 million per transaction without holds, freezes, or manual reviews. Perfect for businesses managing large invoices or supplier payments.

No Plaid Required

Nickel skips the Plaid connection many other platforms rely on. Just use a bank routing and account number to send or receive funds. It’s compatible with 14,000+ U.S. banks.

Branded Payment Links

Easily accept payments without an ecommerce storefront. Create secure, branded links and send them via email, text, or social media. Customers don’t need a Nickel account to pay.

Real-Time Payment Tracking and Settlement

Every payment settles individually, not in batches. That means easier bank reconciliation and real-time status updates so you’re never left guessing.

Recurring and Partial Payment Support

Nickel gives your customers flexibility. Accept partial payments, overpayments, or set up recurring billing with zero manual effort. Every update reflects instantly in QuickBooks.

Pros 

• 100% free ACH transfers with no cap or usage limit
• Native QuickBooks Online integration for seamless syncing
• No need to abandon QuickBooks accounting software
• High transaction limits up to $1 million per payment
• No Plaid dependency
• Secure, shareable payment links with no account sign-up
• Support for credit cards and check deposits
• Individual transaction settlement for easier reconciliation
• Automatic invoice and bill syncing
• Recurring billing and partial payment functionality
• 4.9/5 user rating from thousands of small businesses
• Live support and white-glove onboarding

Cons 

• Only integrates with QuickBooks Online, not QuickBooks Desktop
• Does not support international ACH at this time

Start using Nickel’s 100% free ACH transfers and save countless dollars for your growing business. 

2. Stripe

Stripe is one of the most trusted names in online payments. Its sleek interface, developer-friendly tools, and global reach make it a go-to for SaaS platforms, subscription services, and growing eCommerce brands. 

That said, if your business regularly accepts large invoice payments via ACH, like a manufacturer, wholesale distributor, or bookkeeper, Stripe’s fees can eat into your margins.

ACH transfers on Stripe come with a 0.8% fee, capped at $5 per transaction. That may seem modest, but at scale, those fees stack up quickly. Accepting 100 payments a month? You’re paying up to $500 just to receive money you’ve already earned. 

Stripe does support both QuickBooks Online and QuickBooks Desktop through third-party integrations, which helps with reconciliation, but it’s still a more hands-on setup compared to fully native options.

Stripe Features and Benefits

Stripe features global payment acceptance, ACH debit support, and developer-first APIs that make it a viable QuickBooks Payments alternative.

Global Payment Acceptance

Accept payments in over 135 currencies, with support for cards, bank transfers, wallets, and more, making it ideal for businesses with international customers.

ACH Debit Support (With Fees)

Stripe allows ACH debit payments at 0.8% per transaction, with a $5 cap. There are also fees for failed or disputed transactions.

Powerful Developer Tools

Stripe’s APIs are built for flexibility. Automate billing, customize payment flows, and embed checkout buttons across platforms with ease.

Stripe Invoicing

Send branded invoices and accept ACH or card payments directly through Stripe. This works well, but lacks the advanced accounting tools found in dedicated platforms.

QuickBooks Integration

Stripe supports both QuickBooks Online and QuickBooks Desktop through third-party apps. While it works, the syncing process isn’t always easy and may require manual cleanup.

Pros 

• Accepts payments in 135+ currencies
• Reliable ACH and card processing
• Excellent API documentation for developers
• Strong fraud protection via Stripe Radar
• Compatible with QuickBooks Online and Desktop

Cons 

• 0.8% ACH fee per transaction (capped at $5)
• No native QuickBooks integration - requires third-party tools
• Not ideal for high-volume ACH billing where fee-free processing is essential

3. Melio

Melio has quickly gained traction as a go-to accounts payable and receivable platform for small businesses, bookkeepers, and firms that rely heavily on QuickBooks. With tools built specifically for managing vendor payments, invoicing, and AR/AP workflows, it’s easy to see why so many businesses are considering it as an alternative to QuickBooks Payments. 

It offers native integration with QuickBooks Online and Desktop, along with international payments, approval workflows, and custom payment links. 

But Melio's fee structure, particularly after hitting free ACH limits, makes it better suited to businesses with moderate transaction volume rather than those processing large amounts daily.

What makes Melio stand out is the combination of automation, vendor flexibility, and cash flow control. Still, the benefits vary significantly based on which pricing plan you're on. Below, we’ll discuss the features that make Melio worth considering and where it falls short compared to other options.

Features and Benefits

Melio has several features, such as a certain number of free ACH transfers, that make it a viable QuickBooks Payments alternative. 

Free ACH Transfers With Limits

Melio offers 5 to 50 free ACH transfers per month, depending on your plan. After that, each additional outgoing ACH transfer costs $0.50. Incoming ACH transfers are free only until the plan limit is reached as well, after which a 0.5% fee is applied. Businesses with higher volume may see costs add up quickly if they exceed these limits regularly.

Fast ACH Transfers

Melio gives users the option to upgrade to Fast ACH for quicker settlement, at a cost of 1% of the transaction value, with a cap of $75. This feature is ideal for businesses that need same-day access to incoming funds but don’t want to rely solely on slower, free-tier transfers.

QuickBooks and Xero Integration

Melio offers native integration with both QuickBooks Online and QuickBooks Desktop, plus Xero. That said, the Free plan limits you to syncing just 10 records, which can be a bottleneck for accountants or firms managing multiple transactions daily.

Flexible Vendor Payment Options

You can pay vendors via ACH, check, or credit card, even if the vendor doesn’t accept cards directly. This flexibility helps businesses manage cash flow more effectively by allowing payments through the method that fits their current balance or funding source.

AR Features and Custom Payment Links

Melio allows businesses to create custom payment links for invoices. After setting up a merchant account, customers can pay via ACH or card, and businesses can choose who pays the card processing fee. It's fast, flexible, and ideal for streamlining receivables.

Pros

• Native integration with QuickBooks Online and Desktop
• Free ACH transfers included in all plans (to a certain degree)
• Flexible vendor payment methods, including card and global transfers
• Strong AR tools, including payment links and invoicing
• Mobile app with batch scheduling and approval workflows

Cons

• Free plan only allows 10 synced records with QuickBooks
• $.50 per outgoing ACH after plan limits
• 0.5% fee for incoming ACH after free tier usage
• 1% fee for same-day ACH with a $75 cap
• Approval workflows not available on Free plan

4. Square

Square has built a reputation for being user-friendly and built for small businesses, but it’s not exactly free. While it’s easier to set up and simpler to use than QuickBooks Payments, the fees can still cut deep, especially for businesses that process high volumes or large transactions. 

And with ACH transfers costing 1% (the same as QuickBooks Payments), you’re not escaping the payment toll booth.

Still, Square does bring a lot to the table. It’s ideal for retailers, cafes, and service-based businesses that want an all-in-one POS and invoicing platform. 

If you’re selling online or in-store and want fast setup, real-time payment tracking, and sleek hardware options, Square is hard to beat. But if you’re a manufacturer, bookkeeper, or wholesaler accepting large client payments regularly? You’ll want to read the fine print.

Features and Benefits

Square offers a range of valuable features for businesses that require cost-effective transfers, with integrated invoicing tools being just one of them.

Integrated POS and Invoicing Tools

Square offers built-in point-of-sale tools, invoicing, and inventory tracking without the need for third-party add-ons. Everything works out of the box and syncs smoothly.

QuickBooks Integration (Sort Of) 

Square can sync with QuickBooks Online via a third-party app like Commerce Sync, but it’s not a native integration. Expect to pay extra and handle occasional syncing delays.

Online and In-Person Payments 

Accept payments on your website, over email, or in person using Square’s terminals and readers. It's especially useful for storefronts or service pros.

Recurring Billing and Subscriptions 

Easily set up recurring invoices, payment plans, and automatic billing for ongoing client work. Perfect for freelancers or service-based billing models.

No Monthly Fee (But You’ll Pay in Transfer Fees)

Square’s core offering is free to use, but the fees are baked into every transaction, especially if you rely on ACH or large invoices.

Pros

• Easy setup and intuitive interface for non-tech users
• Works well for retail and service-based businesses
• In-person and mobile payments supported out of the box
• Includes online store builder at no extra cost

Cons

• ACH transfer fee is 1%-same as QuickBooks Payments
• No free ACH allowance like other competitors
• No native QuickBooks Desktop integration
• Fees for instant deposit and recurring billing add up
• Limited support for businesses with large B2B payments

Why Nickel Stands Out as the Best QuickBooks Payments Alternative

Nickel fixes what QuickBooks Payments, Stripe, Melio, and Square still get wrong. It offers unlimited free ACH transfers, easy QuickBooks sync, and full transparency without the usual fine print. For B2B businesses, especially, it’s a smart replacement that reduces fees and friction in one move.

Unlimited Free ACH Transfers Beat Stripe, Melio, and Square

Nickel allows truly unlimited ACH payments and deposits at no cost. Stripe charges 0.8% for ACH. Melio gives you 5 or 50 free transfers, depending on the plan, then hits you with $0.50 per outgoing ACH and 0.5% for incoming. Square doesn’t even offer free incoming transfers.

Nickel’s ACH system also works without Plaid, using just bank account and routing numbers. Businesses can process payments up to $1 million each, something most competitors can’t match.

QuickBooks Sync Without Limitations or Delays

Nickel’s native QuickBooks integration syncs invoices, bills, and payments automatically. Unlike Melio, which limits syncing to 10 records on the Free plan, or Stripe, which often requires developer configuration, Nickel just works, all with no monthly fees or API headaches. This is a big deal for bookkeepers managing multiple clients or high volumes.

Same-Day ACH and Scalable Payouts With No Surprises

Need funds fast? Nickel offers same-day ACH for a 1% fee (capped at $75), similar to Melio’s expedited ACH. But unlike Square or Stripe, Nickel doesn’t hold funds in batched settlements or trigger surprise delays.

Each transaction is settled individually and shows up with a custom statement descriptor, a huge win for reconciliation.

One Platform for A/R and A/P - Without Penalty Fees

With Nickel, outgoing Bill Pay transfers are also free. That means you’re not just getting paid with zero fees, you’re paying vendors the same way. 

Melio charges $1.50 to mail checks, $0.50 per ACH after the limit, and locks A/P approvals behind a paid plan. Stripe and Square don’t even offer full A/P functionality.

Nickel gives you both accounts receivable and accounts payable workflows in one place, with no caps, no hidden restrictions, and no setup delays.

Get started with Nickel today. 

Integrating Nickel With QuickBooks: What to Expect

You don’t have to overhaul your accounting system to stop paying high transaction fees. Nickel works alongside your existing QuickBooks setup, syncing in real time with zero disruption. You get the exact same invoicing and bookkeeping workflows, just without the hidden fees.

The integration takes less than five minutes to activate. Once connected, Nickel automatically updates QuickBooks with payment and billing activity, syncing customers, vendors, invoices, and bills without any manual entry. Payments are settled individually, not in confusing batch deposits, making bank reconciliation faster and cleaner.

For bookkeepers, the benefits are even clearer. You can manage multiple clients in Nickel while keeping all payment data up to date in QuickBooks. This helps maintain efficiency, reduce errors, and eliminate tedious double work.

Most businesses start saving money immediately, especially those handling large or frequent ACH payments. 

How to Sync Nickel With QuickBooks

Follow these simple steps to connect your Nickel and QuickBooks accounts in just a few minutes:

1. Log into your Nickel account and go to Account Settings
2. Click Connect with QuickBooks
3. Sign in to your QuickBooks Online account
4. Select the company you want to connect and choose the correct Chart of Accounts
5. Confirm the sync to automatically import and match your invoices, bills, vendors, and payments
   

Once connected, the sync runs continuously in the background. You can auto-send invoices, track partial payments, update vendor info, and reconcile transactions in real time, all without limits or hidden sync fees. 

Stop Paying Unnecessary Fees: 100% Free ACH Transfers With Nickel 

QuickBooks may keep your books clean, but its payment processing fees are quietly draining your margins. That 1% ACH fee with no cap adds up fast, especially for businesses sending or receiving high-value transactions. 

The good news is you don’t have to abandon QuickBooks to fix the problem. 

Platforms like Nickel give you unlimited free ACH transfers, real-time QuickBooks sync, and enterprise-grade payment features without the price tag. It’s built for small businesses that move big money. Switching to a zero-fee processor like Nickel can save you thousands every year.

Ready to eliminate your QuickBooks Payments fees? Get started with Nickel's free ACH processing and start keeping more of your hard-earned money.

Frequently Asked Questions

How Do ACH Fees Affect My Bottom Line?

ACH fees may seem small, but they scale quickly. A 1% fee on a $300,000 transfer means losing $3,000. Over time, those costs seriously impact profit. Nickel eliminates these fees completely.

Is Nickel Safe for Large Transactions?

Yes. Nickel supports secure payments up to $1 million per transaction with no batching, freezing, or holds. Every transfer settles individually with real-time tracking, simplifying reconciliation.

Can I Still Use QuickBooks If I Switch from QuickBooks Payments?

Yes. Nickel integrates directly with QuickBooks Online. You can keep using your current accounting workflows while Nickel handles the payments and automatically syncs all activity.

What If I Use QuickBooks Desktop?

Nickel only supports QuickBooks Online. If you're using the Desktop version, you'd need to switch to Online or consider another provider like Melio or Stripe, though those come with added fees or complexity.

How Does Nickel Compare to Melio for Accounts Payable?

Nickel includes unlimited free bill payments via ACH, while Melio charges $0.50 per ACH after hitting plan limits and restricts approval workflows. Nickel is better suited for businesses managing high-volume payables.