Quick Answer: FreshBooks charges 1% per ACH with no cap and Stripe caps ACH at $5. Nickel eliminates ACH fees entirely and supports large invoices, making it the most cost-efficient option for those managing high-value payments.
Key Takeaways
- FreshBooks, Stripe, and Nickel all process payments, but ACH fees have the biggest impact on long-term cost.
- FreshBooks charges 1% with no cap, which becomes expensive quickly on high-value transfers.
- Stripe caps ACH fees at $5, but costs still add up when payment volume increases.
- Nickel eliminates ACH fees entirely, allowing unlimited ACH transfers at no cost.
- To stop wasting thousands on fees, adopt Nickel for payment processing and reinvest those savings into growth.
The Real Cost of Payment Processing for B2B Companies
Large invoices and recurring transfers shouldn’t come with inflated fees - but most platforms make them costly. ACH processing typically costs banks around 26-50 cents, yet providers often add percentage-based fees that quietly drain margins over time.
FreshBooks Payments and Stripe both offer convenience, but their ACH fee structures can turn simple transfers into expensive ones. A 1% fee - or even capped charges - adds up quickly when payments reach five or six figures.
That’s where platforms built for cost efficiency matter most. Eliminating ACH fees and reducing payment friction protects cash flow and makes large transactions more sustainable. When comparing payment processors, the real question isn’t features - it’s how much every transfer actually costs.
FreshBooks Payments vs Stripe: Breaking Down the Numbers
When comparing payment platforms, it’s not just about the features - the real differentiator is how fees stack up on high-value ACH transactions. For B2B companies handling large invoices, even a fraction of a percent can mean thousands of dollars in unnecessary costs each year. Let’s look at how FreshBooks Payments and Stripe approach fees.
FreshBooks Payments: Built for Invoicing, Priced for Profit
FreshBooks Payments makes invoicing easy with built-in accounting tools. Card fees average 2.9% + 30¢ per transaction.
The issue appears with ACH transfers: FreshBooks charges 1% with no cap. A single $25,000 invoice costs $250 in fees. Four per month equals $12,000 a year gone to processing costs alone.
Stripe: Developer-Friendly, Enterprise-Ready, Fee-Heavy
Stripe offers strong developer tools and global acceptance. Card fees are the same as FreshBooks.
For ACH, Stripe charges 0.8% capped at $5 per transaction. Large transfers stay affordable, but fees grow fast with higher transaction counts.
Stripe favors fewer large invoices but penalizes higher-volume payment cycles where small fees multiply quickly.
Comparing Payment Platforms
Note: Pricing accurate as of article publication. Verify current rates with each provider.
Why Traditional Processors Fall Short for B2B
FreshBooks and Stripe work well, but their pricing structures weren’t built for high-value transfers. When percentage-based ACH fees are applied to large invoices, margins shrink quickly.
A $45,000 client payment processed through FreshBooks costs $450 in ACH fees alone. Send $30,000 to a vendor the same way, and that’s another $300. In a single billing cycle, $750 disappears simply for moving money - without adding any real value.
For companies managing frequent, high-dollar transfers, losing even 1% to fees puts pressure on cash flow and profitability. Over time, those routine payments can drain thousands that could otherwise support operations, hiring, or growth.
The Nickel Difference: Built for How B2B Actually Works
FreshBooks and Stripe use pricing models suited to smaller consumer transactions. Nickel takes a different approach by eliminating ACH fees entirely - no caps, percentages, or surprise charges.
For invoice-based payments, paying a cut of every transfer drains cash flow fast. Nickel keeps ACH free whether the transfer is $1,000 or $1,000,000, making it practical for anyone managing larger invoices or steady payment cycles.
Credit card processing stays at a flat 2.9% since interchange fees are standard, but ACH remains free across all volumes. Direct QuickBooks integration also streamlines reconciliation without plugins or manual matching, which saves time as well as money.
For anyone tired of losing margin to routine bank transfers, Nickel shifts the economics back in your favor.
FreshBooks Payments: Pros and Cons
FreshBooks Payments appeals to thosealready embedded in the FreshBooks ecosystem, but its fee structure creates challenges for larger transactions.
Pros
- Seamless FreshBooks Integration: Works natively with FreshBooks accounting for an easy setup
- Automatic Reconciliation: Payments automatically match invoices, reducing bookkeeping tasks
- Professional Invoice Presentation: Clean, branded payment pages maintain a polished business image
- Recurring Billing Support: Ideal for retainers, service contracts, or subscription clients
- Multi-Currency Support: Accept payments from international clients (conversion fees apply)
Cons
- Expensive ACH Fees: 1% per transfer with no cap makes large B2B invoices costly
- Platform Lock-In: Only works with FreshBooks accounting, limiting flexibility
- Limited B2B Features: No robust tools for purchase orders or vendor management
- No Check Processing: Cannot handle paper checks still common in B2B
- Basic Approval Workflows: Lacks multi-user approval chains required by larger organizations
Stripe: Pros and Cons for B2B
Stripe is best known for its powerful APIs and global reach but can be more than many B2B companies need.
Pros
- Powerful API: Supports custom payment flows and advanced automation
- Global Reach: Accepts payments in 135+ currencies across 45+ countries
- Subscription Management: Strong tools for SaaS or recurring billing models
- Developer Ecosystem: Extensive documentation and third-party integrations
- Fraud Protection: Machine learning systems that identify and block suspicious activity
Cons
- Technical Complexity: Requires developer resources for implementation and maintenance
- ACH Fees Add Up: Even with the $5 cap, high transaction counts still cost businesses thousands annually
- Overkill for Simple B2B: Many features designed for e-commerce, not invoice-based payments
- Support Challenges: Difficult to reach live support, often self-service only
- Hidden Costs: International fees, currency conversion, and premium tools add expense
Nickel: Pros and Cons for B2B
Nickel is built specifically for how B2B transactions work, offering features that align with high-value invoices and complex cash flows.
Pros
- Free ACH Transfers: Unlimited, uncapped ACH payments with zero fees
- QuickBooks Integration: Direct syncing without changing accounting platforms
- Check Handling: Processes paper checks with scanning and mailing services
- Multi-Client Management: Built for accountants and bookkeepers managing multiple businesses
- Transparent Pricing: No hidden markups or surprise costs for standard services
- Domestic ACH Focus: Specialized in the payment type most common for U.S. B2B transactions
- Vendor and AP Support: Handles both receivables and payables, reducing platform switching
- Simplified Onboarding: Easy account setup without extensive technical integration
- Cash Flow Improvement: By eliminating ACH fees and offering trade credit, businesses preserve margins and liquidity
Cons
- U.S.-Only Availability: Not yet suitable for international payments
- Limited API Tools: Not as developer-focused as Stripe for custom workflows
- No FreshBooks Integration: Connects directly with QuickBooks but not FreshBooks
Real-World Cost Comparison: What This Means for Your Business
Let's run real numbers for a typical company processing $200,000 monthly in payments, with 70% coming through ACH and 30% through credit cards:
(Monthly ACH volume: $140,000/Monthly credit card volume: $60,000)
With FreshBooks Payments
- ACH fees (1%): $1,400
- Credit card fees (2.9% + 30¢): $1,740 + fees
- Monthly total: ~$3,140
- Annual cost: ~$37,680
With Stripe
- ACH fees (0.8%, $5 cap, ~28 transactions): $140
- Credit card fees (2.9% + 30¢): $1,740 + fees
- Monthly total: ~$1,880
- Annual cost: ~$22,560
With Nickel
- ACH fees: $0
- Credit card fees (2.9%): $1,740
- Monthly total: $1,740
- Annual cost: ~$20,880
With Nickel - that's a $16,800 annual difference compared to FreshBooks Payments. For many SMBs, that's enough to hire part-time help, upgrade equipment, or expand inventory. Even compared to Stripe's capped ACH fees, you're saving $1,680 annually - and that's with relatively modest transaction volumes.
Now, if your businesses were to switch to using only ACH transfers for all transactions through Nickel, this would effectively reduce the costs to $0. Consider that if you were to use FreshBooks Payments to move $200,000 in ACH per month, or $2.4 million annually, this would cost you $24,000 in fees per year, compared to the 100% free ACH transfers available through Nickel.
Integration and Workflow Considerations
Choosing a payment platform isn’t just about fees. It affects how efficiently you operate every day, so it’s worth comparing how each one fits into real workflows.
FreshBooks Payments
Integrates directly with FreshBooks accounting and keeps everything in one place. That convenience works if you already use FreshBooks, but it locks you into their system and makes it harder - and more expensive - to scale beyond it.
Stripe
Built for customization. Its API connects with nearly any platform, which is great for complex or developer-led workflows. But if you don’t have technical resources, much of its flexibility can go unused.
Nickel
Integrates directly with QuickBooks while staying open and flexible. You can pair it with FreshBooks, QuickBooks, or even manual processes. Payment links, invoice matching, and reconciliation are automated without forcing you into a closed ecosystem—giving you efficiency without long-term lock-in.
The Bottom Line: Choose Based on Your Business Reality
Choosing the right payment processor directly shapes profitability. FreshBooks Payments delivers convenience but punishes high-value ACH transfers with uncapped fees.
Stripe’s $5 ACH cap is an improvement, but transaction volume can still push costs into the thousands. Nickel was built with B2B realities in mind, offering unlimited free ACH and QuickBooks integration to improve cash flow.
For those managing large invoices, every percentage point matters. Free ACH and streamlined workflows aren’t just nice to have, they can determine whether your margins stay healthy or erode over time.
Ready to stop paying unnecessary fees on ACH transfers? Explore Nickel's pricing or sign up for a free account to see how much you could save.
Frequently Asked Questions
Can I Use FreshBooks Accounting With Nickel for Payments?
While Nickel does not directly integrate with FreshBooks like FreshBooks Payments does, you can still use both platforms. Process payments through Nickel to avoid ACH fees, then manually reconcile in FreshBooks. The time spent on reconciliation is often worth the thousands saved in fees.
Does Stripe Offer Any Way to Reduce ACH Fees for High-Volume Businesses?
Stripe does offer custom pricing for enterprises processing over $1 million monthly, but you need to negotiate directly with their sales team. Even with volume discounts, you are unlikely to match truly free ACH processing.
How Quickly Do ACH Payments Process Through Each Platform?
Standard ACH typically takes one to three business days across all platforms. Nickel offers same-day ACH options, Stripe provides next-day ACH for an additional fee, and FreshBooks follows standard banking timelines.
Is It Difficult to Switch Payment Processors?
Switching is generally straightforward. The main consideration is updating your customers' saved payment methods and ensuring historical transaction data is properly archived. Most businesses complete the switch within a week.
