QuickBooks might be the household name, but if you're sending large invoices and getting crushed by processing fees, it’s time to ask a tough question: is it really worth it? Spoiler: for many small businesses, it’s not.
QuickBooks does a fine job with basic accounting, but when it comes to payments, the platform takes a bigger bite than you think. And that bite adds up. I've seen businesses save thousands per year just by switching to a more payment-friendly solution.
If you're tired of paying premium fees for average performance, this guide will show you the best QuickBooks alternatives built to save you money, speed up cash flow, and give you back control.
Key Takeaways
- QuickBooks Payments charges 1% ACH fees, which add up fast for businesses processing high-value invoices.
- Payment delays and limited automation slow down growing companies that depend on real-time cash flow visibility.
- Specialized platforms like Nickel support advanced features like check printing, large-volume transactions, and fast settlements.
- Most alternatives integrate with QuickBooks Online, allowing you to keep your accounting system while improving your payment tools.
- Industry-specific needs, such as lien tracking, vendor management, or multi-client billing, often go unmet by QuickBooks.
- Hidden costs in other platforms like setup fees, user-based pricing, and volume limits often outweigh any surface-level savings.
- Nickel is the best alternative to QuickBooks if your business wants to eliminate payment fees, speed up collections, and scale with confidence.
Why Small Businesses Are Looking Beyond QuickBooks
QuickBooks has been the go-to for small business accounting for years. But once you’re handling serious volume, like $50,000 invoices or $500,000 in monthly transactions, the cracks start to show.
Business owners are paying attention. Here's why so many are switching to alternatives built for growth.
The 1% ACH Fee Problem
Let’s do the math: QuickBooks charges a 1% fee on every ACH payment you receive. That’s $500 gone on a single $50,000 invoice, just to accept money.
Most people don’t realize the actual ACH processing cost is usually less than $0.50 per transaction. That makes percentage-based ACH fees one of the most expensive and unnecessary costs a growing business can face.
Processing Delays
On that note, many disgruntled former customers note just how slow QuickBooks ACH transfers can be, sometimes taking a week or more for funds to arrive. When you’re making or receiving payments, you just don’t have that kind of time to wait around.
Limited Payment Flexibility
If you’re still using QuickBooks Payments for anything beyond basic invoicing, you’ve probably hit a wall. Businesses handling complex B2B transactions often need:
- Multi-step approval workflows
- Check printing and mailing options
- Vendor payment scheduling
- Multi-client billing tools for bookkeepers and accounting firms
QuickBooks doesn’t offer much here. And when your operations expand, those limitations slow you down.
Cash Flow Constraints
Waiting 30 to 60 days for clients to pay while bills pile up? Join the club. QuickBooks offers invoices and reminders, but not much else. For businesses managing tight payment cycles, that’s a major problem. You need smarter tools that help bridge the gap, not just track it.
Top Alternatives to QuickBooks for Small Business Payment Processing
Here are the top four alternatives to QuickBooks for small business payment processing.
1. Nickel - Best for B2B Payment Processing
If you’re tired of ACH fees eating into your margins, Nickel is the payment platform your business has been waiting for. It’s built from the ground up for high-value B2B transactions, and it outclasses QuickBooks Payments on every front, especially when it comes to ACH payments.
Here’s Why 10,000+ Businesses Have Already Made the Switch
- Unlimited free ACH transfers with no per-transaction fees or volume caps
- High-value transaction support up to $1 million per payment, without holds
- 2x faster settlements than traditional ACH processors
- No Plaid required; just routing and account numbers
- Real-time QuickBooks sync that updates payments and invoices instantly
- One-to-one bank reconciliation with clear, itemized settlement reporting
- Built-in check processing for scanning and mailing physical checks
- Credit card support at 2.9% flat, with fee pass-through options
- Transparent pricing structure
Nickel’s native QuickBooks integration connects in under five minutes and doesn’t disrupt your existing workflows. Every invoice, bill, and customer record syncs automatically. You can even match partial payments, track overpayments, and reconcile your bank statements without spreadsheets or batch reports.
Best For: Contractors, accounting firms, manufacturers, and service providers handling $50K to $1M+ per month in B2B volume
Pricing: $0 monthly fee. Free ACH. Flat 2.9% credit card processing. Check mailing from $2 per check.
Bottom Line: If you’re running a serious B2B business, QuickBooks Payments is holding you back, and Nickel is the upgrade you’ve been waiting for.
2. Xero - Strong International Features
Xero is a cloud-based accounting platform that stands out for its global reach and collaborative tools. It’s especially useful for companies operating in multiple currencies or regions, with flexible access for teams and accountants.
Core Features
- Multi-currency support with automatic exchange rate updates
- Real-time collaboration with accountants and bookkeepers
- Bank reconciliation and financial reporting
- Inventory tracking, W-9 and 1099 contractor management
- Integration with Gusto payroll and third-party apps like Stripe, Hubdoc, and GoCardless
Best For: Businesses with international operations, remote finance teams, or those needing strong multi-user collaboration features.
Limitations
- ACH payment fees vary depending on the payment method and can be quite high.
- For invoice payments, fees are typically $1 per ACH transaction.
- For bill pay, fees range from 0.5% + $0.25 (capped at $6) to $0.49 per bill. ACH returns and chargebacks can trigger additional fees.
- Xero also lacks built-in tools for check mailing, advanced B2B approvals, or zero-fee high-value transfers.
- Also, features like payment scheduling and high-volume workflows require multiple integrations.
Pricing: Early Plan: $20/month, Growing Plan: $47/month, Established Plan: $80/month. All plans include a free 30-day trial. Online payments and bill pay are optional and subject to transaction fees.
3. FreshBooks - Service-Based Business Focus
FreshBooks is a cloud-based accounting platform built with freelancers and service-based businesses in mind. Its strength lies in user-friendly invoicing, time tracking, and client collaboration, all packaged in an interface that’s easy to navigate and tailored to solo professionals and small teams.
Core Features
- Professional, customizable invoices with automated reminders
- Built-in time tracking and expense management
- Client portal for approvals, payments, and document sharing
- Project management and profitability tracking
- ACH and credit card payments with automatic reconciliation
- Integrates with Gusto, Stripe, Bench, and over 100 apps
Best For: Freelancers, consultants, creative professionals, and agencies managing recurring work and client relationships.
Limitations
- FreshBooks isn’t well-suited for businesses with inventory or complex B2B payment needs.
- ACH fees are 1% per transaction, and credit card processing starts at 2.9% + $0.30.
- Advanced payment features and additional team members require extra fees.
- No built-in tools for mailing checks or zero-fee transfers.
Pricing: Lite Plan: $21/month (up to 5 clients), Plus Plan: $38/month (up to 50 clients), Premium Plan: $65/month (unlimited clients), Select Plan: Custom pricing with volume discounts and premium support. There is a free 30-day trial available.
- Add-ons include Advanced Payments ($20/month) and team members ($11/month per user).
If you’re a business handling complex invoices and payments, you process large volumes and high-value transactions, and you need those ACH fees to be non-existent, Nickel is the far better alternative to QuickBooks.
4. Wave Accounting - Free Basic Features
Wave is a no-cost accounting solution designed for freelancers and very small businesses. Its free starter plan includes invoicing, basic bookkeeping, and receipt scanning, making it one of the few truly free platforms in the space. While it lacks advanced automation and payment flexibility, it delivers solid value for service-based entrepreneurs just starting out.
Core Features
- Unlimited invoicing, estimates, and bookkeeping records
- Accepts credit cards, ACH, and Apple Pay (with fees)
- Automatic reminders and recurring billing options
- Digital receipt capture (with paid add-on)
- Dashboard insights and customizable templates
- Mobile invoicing and customer tracking
Best For: Solo entrepreneurs, gig workers, and freelancers who need simple invoicing and accounting tools with minimal overhead.
Limitations
- Lacks robust features like check payments, approval workflows, and cash flow forecasting.
- Most automation tools are behind the Pro Plan.
- Wave’s ACH fees are 1% per transaction with a $1 minimum, which adds up fast on large payments.
- Credit card fees start at 2.9% + $0.60 per transaction on the free plan.
Pricing: Starter Plan: Free, Pro Plan: $16/month
- Optional Add-ons: Receipts: $8/month, Payroll: from $20/month, Bookkeeping: from $149/month.
Financial Impact: The Real Cost of Sticking with QuickBooks Payments
Let's examine what QuickBooks' payment processing fees actually cost different types of businesses:
Construction Supply Company (Processing $200K monthly)
- QuickBooks ACH fees: $2,000/month or $24,000 annually
- Nickel's free ACH processing: $0
- Annual savings: $24,000
Wholesale Distributor (Processing $500K monthly)
- QuickBooks ACH fees: $5,000/month or $60,000 annually
- Free alternative: $0
- Annual savings: $60,000
Bookkeeping Firm (Managing 20 clients, $50K average monthly volume per client)
- QuickBooks fees across all clients: $10,000/month or $120,000 annually
- Multi-client solution with free ACH: $0
- Annual savings: $120,000
These aren't hypothetical numbers. They represent real costs that businesses pay every month for basic payment processing. Remember, Nickel allows for 100% free and unlimited ACH transfers, both incoming and outgoing.
Making the Switch: What to Consider
Switching from QuickBooks Payments doesn't have to mean ditching QuickBooks entirely. In fact, many small businesses stick with QuickBooks for accounting and simply replace its payment processing with a more affordable, specialized solution.
Here’s what you need to think about when making the switch:
Integration Requirements
You can keep your familiar QuickBooks workflow while cutting payment costs. Platforms like Nickel integrate directly with QuickBooks Online, allowing you to:
- Continue using QuickBooks for day-to-day accounting
- Add better payment features like custom approvals and real-time tracking
- Sync invoices, customer data, and payment records automatically
There’s no need to rebuild your accounting system. You just plug in a better payment engine.
Data Migration
If you're using QuickBooks for accounting and switching payment platforms, you typically won’t need to migrate data at all. Payment-focused tools sync with your existing records inside QuickBooks, so setup is fast and low risk.
Training and Adoption
Most alternatives are designed to be intuitive. You’re not learning a new accounting system, you’re just changing how you get paid. For most teams, the only real adjustment is setting up new approval steps or ACH preferences. Once that's done, it's business as usual, only faster and cheaper.
Industry-Specific Considerations
Not all businesses run the same way, and your payment platform shouldn’t either. Different industries have different needs, and QuickBooks doesn’t always keep up. Let’s look at three key sectors where a better payment system makes a real impact.
Construction and Contracting
Contractors deal with more than just sending invoices. You’ve got lien deadlines, payment draws, and multiple subcontractors to coordinate. While QuickBooks covers the basics, specialized solutions bring critical tools like:
- Automated lien notice reminders
- Progress billing tied to contract milestones
- Payment scheduling for subcontractors
- Integrated job costing features
These tools help you avoid payment delays, stay compliant, and keep every stakeholder aligned. For a deeper look at payment risk in construction, check out our guide on lien laws and payment timelines.
Wholesale and Distribution
Wholesale operations are fast-moving and high-volume. You’re juggling bulk orders, long payment terms, and vendor payables, all while managing razor-thin margins. QuickBooks Payments simply doesn’t cut it here. B2B-focused payment systems offer better tools for:
- Processing large-volume transactions
- Managing Net 30 or Net 60 terms
- Automating payables across multiple vendors
- Tracking incoming payments to support cash flow
The result is fewer headaches, fewer late payments, and fewer cash flow surprises.
Professional Services and Bookkeeping
If you run a bookkeeping firm or offer consulting services, you're probably managing payments for more than one client. QuickBooks lacks the flexibility needed for multi-client billing environments. Smart alternatives provide:
- Unified dashboards across client accounts
- Batch invoicing and payments
- Consolidated reporting by client or project
- Lower transaction costs to preserve your profit margins
This helps you scale your service without wasting time on repetitive admin work—or losing money to processing fees.
The Hidden Costs of QuickBooks Alternatives
Not every QuickBooks alternative is actually cheaper in the long run. In fact, many of the so-called “cost-saving” options quietly tack on fees that add up fast. Before you switch, take a closer look at these often-overlooked costs, and compare them to what a focused solution like Nickel offers.
Setup and Migration Fees
Some platforms will hit you with onboarding costs right out of the gate. That might include data imports, account configuration, or custom integration fees. These can easily climb into the hundreds, especially if you need help moving historical records.
Nickel skips the fluff and offers a fast onboarding process with zero setup fees, so you can get started without blowing your budget.
Per-User Pricing
Accounting software often charges you based on how many people access the system. As your business grows, so do your costs. What starts at $20 per month can snowball into $100 or more just by adding a few team members.
Transaction Volume Limits
Many “free” tools come with strings attached. You might be limited to a few dozen transactions per month, which sounds fine until you start scaling. Then come the overage fees.
Nickel gives you unlimited invoice processing with no artificial limits. Whether you send five invoices a month or five hundred, your fees don’t change.
Integration Costs
If your software doesn’t natively integrate with your accounting system, you’ll end up patching things together with third-party tools. These integrations aren’t just annoying; they often come with monthly subscription costs and extra setup time.
Nickel integrates directly with QuickBooks Online, eliminating the need for third-party connectors or manual syncing. That means fewer apps, less confusion, and lower total costs.
Future-Proofing Your Payment Processing
Don’t just think about what works today. Think about what’s still going to work when your business hits its next revenue milestone. The right QuickBooks alternative shouldn’t just support your current operations.
It should grow with you, adapt to your needs, and keep you compliant every step of the way. Here’s what to watch for when evaluating long-term options.
Scalability
If your payment system starts glitching once you pass 50 clients or delays deposits when volume spikes, that’s a red flag. A future-proof platform needs to handle everything from five-figure months to eight-figure years without skipping a beat. Nickel was built to scale, offering reliable performance even as invoice volumes increase dramatically.
Feature Development
A stagnant platform is a liability. You want a provider that’s always shipping useful updates, not just cosmetic changes. Look for consistent product improvements focused on B2B payment automation, advanced approval workflows, and better fraud prevention.
Regulatory Compliance
ACH regulations and payment industry rules are always evolving. Falling out of step with compliance can freeze your funds or trigger costly reviews. Your provider should handle things like NACHA rules, data encryption standards, and Know Your Customer (KYC) updates behind the scenes.
Industry Focus
Not every platform is built with your business model in mind. For example, B2B service providers need invoicing flexibility, while wholesalers prioritize large transaction batching. Choose a provider that understands your industry’s workflows. Nickel is purpose-built for invoice-heavy businesses that need speed, visibility, and control over payments.
Real Business Impact
Let’s get real for a second. This isn’t just about software features or fancy dashboards. It’s about what hits your bottom line.
One wholesale distributor we spoke to was processing around $800,000 a month through QuickBooks Payments. With ACH fees adding up to $8,000 every month, they were shelling out $96,000 a year just to receive money. No joke.
After switching to Nickel, those fees disappeared. They also gained better visibility into vendor payments, simplified check handling, and eliminated reconciliation delays. The cost savings? Enough to pay for a brand-new delivery truck.
These are the kinds of operational wins that save money and unlock growth. That’s the difference a purpose-built platform like Nickel can make when you're running large B2B transactions at scale.
Making Your Decision
Picking the right alternative to QuickBooks depends on where your pain points are. Here are a few smart ways to approach the decision:
- If you’re drowning in fees, prioritize platforms with truly free ACH payments. Bonus points if they support large transactions without extra charges or volume caps.
- If you rely on invoice-based billing, choose tools built for B2B payment flows, especially ones that support net terms, partial payments, and client-specific rules.
- If you manage multiple client accounts, you’ll need multi-entity dashboards and bulk payment tools. QuickBooks can’t do this well, but Nickel can.
- If your cash flow is tight, look for payment advance features or automated net terms that can help you get paid faster and stay liquid.
Here’s the bottom line: don’t just compare monthly subscription prices. Run the numbers on your total cost of ownership, including ACH fees, credit card processing rates, hidden reconciliation costs, and time lost managing payments manually.
And if those numbers make you cringe? It’s time to switch to Nickel.
Taking Action
If you're paying thousands in ACH fees just to get paid, it's time to rethink your payment stack. QuickBooks might work for basic accounting, but it falls flat once you start handling serious B2B volume. You don’t need to ditch your entire system, you just need a better way to move money.
That’s where platforms like Nickel come in handy. Free ACH, faster settlements, better payment tracking, and deep QuickBooks integration make it a smarter way to run your business. The truth is, you’ve already outgrown QuickBooks Payments. And now, there’s a better option sitting right in front of you. Make the switch. Get your margins back.
Ready to eliminate unnecessary payment processing fees and streamline your B2B payment operations? Get started with Nickel's free ACH processing and see how much your business could save.
Frequently Asked Questions
What Is the Best Alternative to QuickBooks for B2B Payments?
Nickel is the top choice for B2B businesses processing large invoices. It eliminates ACH fees, speeds up payments, and integrates directly with QuickBooks Online.
Can I Use Nickel With QuickBooks Online?
Yes. Nickel connects directly with QuickBooks Online, syncing invoices, payments, and reconciliation data automatically without disrupting your current accounting workflows.
How Much Can I Save by Switching From QuickBooks Payments?
Many businesses save thousands each year. For example, processing $500K monthly could mean $60,000 in annual savings just from eliminating QuickBooks’ 1% ACH fees.
Do QuickBooks Alternatives Support Check Payments?
Some, like Nickel, include built-in check scanning and mailing tools. Others require third-party add-ons or manual processing, which can be time-consuming and costly.
What Should I Look For in a QuickBooks Alternative?
Focus on ACH fee structure, B2B payment features, scalability, and QuickBooks integration. The best alternatives to QuickBooks should grow with your business without hidden costs.
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