2025 Credit Card Processors for Small Businesses (and How to Reconcile Them in Beancount)

Choosing a credit card processor is part math, part operations. The right partner simplifies your workflow, while the wrong one can slowly bleed your margins through hidden fees and create bookkeeping nightmares. Transaction fees, payout timing, hardware costs, contracts, and data export quality all affect your bottom line—and your accounting workflow. This guide highlights popular U.S. options in 2025 and adds Beancount-friendly tips so you can keep your ledger clean from day one.

All pricing snapshots below are published U.S. rates as of September 2025 and may vary by plan, industry, and transaction volume. Always confirm current pricing on the provider’s official site.

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How to Choose: A Quick Framework

Before diving into brand names, use this framework to narrow your search. Your business's unique transaction profile is the most important factor.

• Transaction Mix

  • Mostly in-person, low average ticket: Your priority is speed and simplicity at the point of sale. Favor simple flat-rate POS systems like Square, Zettle, Clover, or Chase.
  • Mostly online/SaaS or multi-country: You need robust APIs, international payment methods, and developer-friendly tools. Look at Stripe, Adyen, or Braintree.
  • $30k–$100k+ monthly volume with a stable mix: At this scale, flat-rate pricing becomes expensive. It's time to consider interchange-plus (Helcim, Dharma) or membership (Stax, Payment Depot) models to lower your effective rate.

• Total Cost of Ownership (TCO) Don't just look at the advertised percentage. Calculate your effective rate by combining the percentage fee, fixed cents-per-transaction fee, monthly account fees, hardware costs, and potential chargeback fees. This gives you a true picture of your costs.

• Payout Cadence How quickly do you need your cash? A next-day deposit schedule versus a two-day rolling window (T+2) can significantly impact your cash-flow forecasting. We'll cover how to model this in Beancount below.

• Lock-In Avoid long-term contracts with hefty early termination fees (ETFs). Look for month-to-month billing and, crucially, the ability to easily export your transaction data via CSV or an API. Your data is your own; don't let a processor hold it hostage.

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The Shortlist: Who It’s Best For

Stripe — Best for Online-First and Platforms

Stripe is the gold standard for internet businesses. Its excellent APIs, pre-built Checkout and Link components, robust subscription management, and global payment method support make it incredibly versatile. For physical sales, its Terminal line of hardware integrates seamlessly.

• Pricing Snapshot: Online transactions are typically 2.9% + 30¢ (domestic). In-person payments via Terminal are 2.7% + 5¢. International cards and currency conversion may incur surcharges.
• Payouts: Operates on a configurable, rolling schedule. Most U.S. businesses see funds available on a T+2 basis (two business days after the transaction).

Square — Best Turnkey POS for New Storefronts

Square excels at getting new retail and service businesses up and running quickly. With a free and intuitive POS app, a simple hardware lineup, and fast onboarding, it's a favorite for cafes, boutiques, and service providers.

• Pricing Snapshot: In-person is 2.6% + 15¢, online is 2.9% + 30¢, keyed-in is 3.5% + 15¢, and invoices are 3.3% + 30¢.
• Payouts: Standard next-business-day transfers are free. For urgent cash needs, instant or same-day transfers are available for an additional 1.75% fee.

PayPal Zettle — Best “Micro-Merchant” Mobile POS

Perfect for sellers at farmers' markets, pop-up shops, or conventions. Zettle offers low-cost entry hardware that integrates smoothly with the broader PayPal ecosystem, making it easy to manage funds alongside your online PayPal sales.

• Pricing Snapshot: In-person card transactions are 2.29% + 9¢. Keyed, invoice, and online transactions have separate rates.

Braintree (by PayPal) — Best for PayPal/Venmo + Cards Under One API

Braintree is a developer-centric platform that allows businesses to accept credit cards, PayPal, Venmo, and other digital wallets through a single integration. It's a strong choice for e-commerce sites that want to offer customers a wide array of payment options.

• Pricing Snapshot: Standard rate for cards and most digital wallets is 2.89% + 29¢. Venmo is often 3.49% + 49¢. Discounts for non-profits and custom pricing for high-volume businesses are available.

Helcim — Best Transparent Interchange-Plus with Volume Discounts

Helcim offers interchange-plus pricing with no monthly fee, making it an accessible option for businesses graduating from flat-rate models. Its pricing automatically gets cheaper as your processing volume increases, with clear tiers published on its site.

• Pricing Snapshot: Margins are typically around Interchange + 0.40% + 8¢ (card-present) and Interchange + 0.50% + 25¢ (card-not-present), with margins decreasing at higher volumes.

Dharma Merchant Services — Best Small-to-Mid B2B Interchange-Plus

Dharma is known for its fair interchange-plus pricing and excellent support, with a focus on B2B transactions. It helps businesses qualify for lower Level 2 and Level 3 processing rates, which can lead to significant savings on corporate card transactions.

• Pricing Snapshot: Card-present is IC + 0.15% + 8¢, and e-commerce is IC + 0.20% + 11¢, plus a modest monthly fee.

Stax — Best Subscription (Membership) Pricing at Higher Volumes

Stax uses a membership model: you pay a flat monthly subscription fee and in return get access to direct interchange rates with a "0% markup." This can be extremely cost-effective once your monthly volume is high enough to justify the subscription cost.

• Pricing Snapshot: Plans start at $99/month, with tiers based on annual processing volume.

Payment Depot — Membership Alternative to Lower Processing Costs

Similar to Stax, Payment Depot offers interchange-plus rates under a membership model. It positions itself as a way for businesses to access wholesale processing rates without percentage markups, with an emphasis on no long-term contracts or early termination fees.

• Pricing Snapshot: Membership-style IC+ pricing. Plans are typically provided via a custom quote.

Shopify Payments — Best if You Already Run on Shopify

If your business runs on Shopify, using Shopify Payments is a no-brainer. It's tightly integrated with your store, provides excellent fraud analysis tools, and enables the high-converting Shop Pay checkout. Using a third-party gateway on Shopify incurs additional fees.

• Pricing Snapshot: Rates are tied to your Shopify plan. Online fees range from ~2.5% to 2.9% + 30¢, while in-person rates are around 2.4% to 2.6% + 10¢ on higher tiers.

Toast — Best All-in-One for Restaurants

Toast is purpose-built for the food and beverage industry. Its platform combines durable, restaurant-grade hardware with software for kitchen display systems (KDS), online ordering, inventory, and even payroll add-ons.

• Pricing Snapshot: A pay-as-you-go plan is available at ~3.09%–3.69% + 15¢. If you pay for hardware upfront, rates can be as low as 2.49% + 15¢ (card-present) and 3.50% + 15¢ (card-not-present).

Clover (Fiserv) — Best POS Hardware Variety (Retail/Service)

Clover offers one of the broadest hardware lineups in the industry, from the mobile Go and Flex to the countertop Mini and Station. This variety makes it a flexible choice for retail stores and service businesses that need a specific form factor.

• Pricing Snapshot: Rates vary widely by plan and device, but in-person rates are commonly advertised as low as 2.6% + 10¢.

Lightspeed Payments — Best Mid-Market Retail POS with Deep Inventory

Lightspeed is a powerhouse for retail businesses with complex inventory needs. Its integrated payments system works seamlessly with its advanced POS features, providing a unified platform for sales and stock management.

• Pricing Snapshot: A frequently cited U.S. reference rate is ~2.6% + 10¢ for in-person and ~2.9% + 30¢ for card-not-present transactions.

Authorize.Net — Best Standalone Gateway (Bring Your Own Merchant Account)

A long-standing and trusted name, Authorize.Net is a payment gateway that connects your website to your merchant account. This is for businesses that have already negotiated a direct merchant account with an acquiring bank and just need the technology layer to process online payments.

• Pricing Snapshot: All-in-one: $25/mo + 2.9$25/mo + 10¢ per transaction, plus a small daily batch fee.

Chase Payment Solutions — Best Bank-Integrated POS & Fast Deposits

For businesses that bank with Chase, their payment solutions offer a compelling advantage: the potential for same-day deposits into a Chase business checking account at no extra cost. This tight integration simplifies cash flow management.

• Pricing Snapshot: Card-present is 2.6% + 10¢, while keyed-in sales and payment links are 3.5% + 10¢.

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Beancount: Model Your Payouts and Fees Cleanly

Plain-text accounting shines when you can model real-world financial flows precisely. For payment processors, the key is using a "clearing account" to track money from the moment of sale until it lands in your bank. This preserves your gross revenue figures and makes reconciliation trivial.

Example Chart of Accounts:

Assets:Bank:Operating
Assets:Processors:Stripe      ; A clearing account for each processor
Income:Sales
Expenses:ProcessingFees
Liabilities:SalesTax:Payable

Pattern A: “Net Deposit” Processors (Most Flat-Rate)

Most processors batch your sales, subtract their fees, and deposit the net amount. Your job is to record the gross sale first, then account for the deposit and the fee. A $100 sale with a$2.90 fee becomes:

2025-09-08 * "Online order #8421"
  Assets:Processors:Stripe               100.00 USD
  Income:Sales                          -100.00 USD

2025-09-09 * "Stripe payout"
  Assets:Bank:Operating                   97.10 USD
  Expenses:ProcessingFees                  2.90 USD
  Assets:Processors:Stripe               -100.00 USD

Why this pattern is essential: It correctly records $100 in `Income:Sales` and$2.90 in Expenses:ProcessingFees. This is critical for analyzing your true gross revenue and is exactly what you need to reconcile your books with the processor's 1099-K form at year-end.

Pattern B: “Daily Batch” with Line-Item Fees

Some POS systems (like Toast or Clover) will show a single large deposit for a day's sales, with fees deducted as separate line items in their report. The principle is the same: balance the clearing account to zero.

2025-09-08 * "Toast batch — store #1"
  Assets:Bank:Operating                  1,943.55 USD
  Expenses:ProcessingFees                   56.45 USD
  Assets:Processors:Toast               -2,000.00 USD

Pattern C: “Membership” Pricing (Stax/Payment Depot)

For membership models, the monthly subscription is a separate operating expense. You book it directly, while the much smaller per-transaction fees are handled using Pattern A or B.

2025-09-01 * "Stax subscription"
  Expenses:ProcessingFees                  99.00 USD
  Assets:Bank:Operating                   -99.00 USD

Importing & Reconciling Tips

• One Clearing Account Per Processor: Create Assets:Processors:Stripe, Assets:Processors:Square, etc. If you have multiple locations, consider Assets:Processors:Toast:Store1 to isolate activity.
• Mind the Payout Cadence: A sale on Friday might not hit your bank until Tuesday. This lag is why the clearing account is so important for accurate cash forecasting.
• Automate Your Imports: Every provider offers CSV exports. Write simple Python scripts or use Fava's importer functionality to map the columns (date, gross amount, fees, net deposit) to Beancount transactions.
• Handle Sales Tax Correctly: Sales tax is not income. Split it out to Liabilities:SalesTax:Payable at the time of sale. Most POS reports provide this breakdown.
• Book Chargebacks Promptly: When a chargeback occurs, the processor debits your account. Book a reversal to Income:Sales for the sale amount and a separate entry to Expenses:ProcessingFees for the chargeback fee.

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Quick Comparison Snapshot

Provider	Pricing model	In-person (from)	Online (from)	Monthly fee	Payout notes
Stripe	Flat‑rate + options	2.7% + 5¢	2.9% + 30¢	$0	Configurable; often ~T+2.
Square	Flat‑rate	2.6% + 15¢	2.9% + 30¢	$0	Next‑day free; instant/same‑day 1.75% transfer fee.
Zettle	Flat‑rate	2.29% + 9¢	Varies	$0	PayPal ecosystem.
Braintree	Flat‑rate / custom	—	2.89% + 29¢	$0	PayPal/Venmo/wallets under one roof.
Helcim	Interchange‑plus	IC + 0.40% + 8¢	IC + 0.50% + 25¢	$0	Volume‑based discounts.
Dharma	Interchange‑plus	IC + 0.15% + 8¢	IC + 0.20% + 11¢	~$20	Level 2/3 for B2B.
Stax	Membership (0% markup)	Interchange + cents	Interchange + cents	From $99	Savings at higher volume.
Payment Depot	Membership IC+	Interchange + cents	Interchange + cents	Quote	Wholesale‑style plans.
Shopify Payments	Flat‑rate	~2.4–2.6% + 10¢	~2.5–2.9% + 30¢	Included	Plan‑dependent rates.
Toast	Flat‑rate (tiered)	2.49% + 15¢	3.50% + 15¢	From $0	Restaurant‑specific suite.
Clover	Flat‑rate (by plan)	as low as 2.6% + 10¢	2.9% + 30¢+	Plan‑based	Wide hardware range.
Lightspeed	Flat‑rate (region)	~2.6% + 10¢	~2.9% + 30¢	POS plan	See regional fee tables.
Authorize.Net	Gateway (or AIO)	—	2.9% + 30¢ (AIO)	$25	Gateway‑only: $25 +$0.10/txn + batch fee.
Chase	Flat‑rate	2.6% + 10¢	3.5% + 10¢	$0	Same‑day deposits to Chase checking at no extra cost.

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Which One Should a Beancount User Pick?

• For the simplest setup with daily auto-payouts: Start with Square or Zettle. Their reports are clean and easy to import.
• For developer work, subscriptions, or multiple payment methods: Stripe or Braintree are your best bets due to their powerful APIs.
• If you process ≥$30k/month with a stable card mix: It's time to do the math. Price out Helcim (IC+) versus Stax/Payment Depot (membership) to calculate your true effective rate.
• For a restaurant POS: Compare Toast and Clover/Lightspeed, paying close attention to contract terms and hardware financing.
• If you're already on Shopify: Use Shopify Payments to avoid paying extra gateway fees.
• For same-day deposits into your operating account: Chase QuickAccept linked to a Chase business checking account is the clear winner.

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Final Beancount Checklist

• Create Assets:Processors:* clearing accounts for each processor and location.
• Always record gross sales and separate fees, even if your bank deposit is a net amount.
• Match payout dates and batch IDs from the processor's CSV report to your clearing account transactions.
• Automate your workflow by writing small importers to map CSV columns to Beancount postings.
• Review chargebacks weekly and post the reversal and fee on the day they are debited by the processor.