Payment processor for a service business that takes a deposit and charges the balance later

Square Invoices is a good starting point for a typical service business: you can request a deposit, set a due date for the remaining balance, and split the balance into scheduled payments. Square also documents charging a card on file when an invoice payment is due. (squareup.com)

If you mean take the deposit at online booking and automatically charge the balance on the appointment date, check the booking software too—whether that works depends on its integration and settings.

Stripe is another option, especially if you have a website or custom booking system. It can charge a saved card later, but you need the customer’s permission, and a bank may sometimes require them to confirm the later charge. (support.stripe.com)

Simple rule of thumb: Square for straightforward invoices and payment schedules; Stripe for a more customized online setup. Which service business are you running, and do you want to charge the balance automatically or send an invoice for it?

Short answer: If you already use QuickBooks Online, QuickBooks Payments is the easiest fit. If you don't, Stripe or Helcim are the main alternatives. Verify rates before you commit, since they change.

QuickBooks Payments (best if you use QuickBooks Online)

• Its estimates let customers approve and pay a deposit at the same step, which fits your model. Lock in projects faster with instantly-payable deposits. Simply send an estimate, and customers approve with a deposit.
• It accepts partial payments, so the balance can be collected later through the same invoice.
• Card invoices cost 2.99%, and deposits arrive faster: the next business day for card payments taken before 3 p.m. PT, against Stripe's two business days.
• Its drawback is that it's pricier for bank transfers. Stripe is cheaper for bank payments: 0.8% capped at $5, against QuickBooks' 1% with no cap published.

Stripe (best if you want flexibility or large ACH payments)

• Stripe is the usual choice when you need custom workflows. Its $5 cap can lower costs once a transaction reaches a certain size.
• Invoicing adds cost. Stripe charges 2.9% + 30¢ plus its 0.4% Invoicing fee, so a $1,000 invoice costs $29.90 on QuickBooks and $33.30 on Stripe.
• Accounting sync is more work. Stripe doesn't offer a direct native integration with QuickBooks.
• Payouts are slower. Stripe pays out two business days after the charge, and its first payout typically takes 7 to 14 days.

Helcim (good for low card costs and no monthly fees)

• It uses interchange-plus pricing, and the virtual terminal and online invoicing come free.
• Sources disagree on deposit speed. One says next-business-morning deposits for credit and debit transactions, while NerdWallet notes that deposits may take up to two business days; same-day deposit option is not available.
• Interchange-plus fees are harder to predict, so ask for a quote on your typical ticket size.

Square (only if you take most payments in person)

• Square's online pricing is higher on its free plan. 3.3% + 30¢ on Square Free; 2.9% + 30¢ on Plus and Premium.

What to check before signing up

• Confirm you can charge a saved card or bank account for the balance without the customer present. Ask each provider this directly, because the sources I found didn't address it.
• Check whether the invoice tool sends automatic reminders for the balance, and whether it handles sales tax on services in your state.
• If you need an accounting-linked invoicing tool that isn't tied to one processor, Harvest integrates with Stripe (credit card and ACH) and PayPal and syncs with QuickBooks and Xero.

Tell me which accounting software you use and whether you bill mostly by card or ACH, and I can narrow this to one recommendation.

For a service business that needs to collect a deposit and charge the balance later, you need a payment processor that supports "Authorize and Capture" (sometimes called "Delayed Capture") or "Saved Payment Methods" (tokenization).

Instead of charging the full amount immediately, these features allow you to verify the customer's payment method, secure a deposit, and then trigger the final charge when the service is complete.

Recommended Payment Processors

The following processors are widely used by service businesses for their flexibility and robust API/dashboard capabilities:

• Stripe: Highly recommended for service businesses due to its developer-friendly tools and ease of use. It allows you to easily "authorize" a card to check for funds and "capture" the final balance later. Its "Saved Payment Methods" feature is excellent for securely storing customer data for later billing without needing to handle sensitive card details yourself.
• Square: An excellent all-in-one solution if you also need point-of-sale (POS) hardware or simple, no-code billing tools. Square provides clear dashboard options to manage deposits and final payments, making it very accessible for small business owners who don't want to deal with complex coding.
• Authorize.net: A long-standing, traditional payment gateway that is very strong in "Authorize and Capture" workflows. It is often a great choice if you prefer a more traditional merchant account setup and need highly configurable payment rules.
• Helcim: Known for its "interchange-plus" pricing, which can be more cost-effective for businesses with higher transaction volumes. It is well-suited for service-based businesses that need professional invoicing and the ability to manage customer payment profiles securely.

Key Features to Look For

When evaluating these providers for your specific workflow, look for these two capabilities:

1. Authorize & Capture (Two-Step Payment): This allows you to verify that the customer’s card is valid and has sufficient funds (the "Authorization") without immediately moving the money. You then "Capture" the funds (or a portion of them) when you are ready to finalize the payment. Note that authorizations typically expire after 7–30 days, so this is best for shorter-term projects.
2. Customer Tokenization (Saved Cards): If your service projects take longer than a few weeks, you should use "tokenization." This lets you securely save the customer's payment information (as a "Customer Profile") in a PCI-compliant way. You can then charge the card for the deposit now and the balance later, even if the final payment is months away.

Implementation Strategy

• If you send invoices: Most modern processors (Stripe, Square, Helcim) integrate with accounting software like QuickBooks or Xero. You can send an invoice that allows the customer to pay the deposit online, and then charge the remaining balance to the saved card on file once the project is finished.
• If you don't use accounting software: You can use the processor’s native dashboard to create "Payment Links" or "Request Payment" features. Simply create a request for the deposit, and for the balance, trigger a new payment charge using the securely stored customer token.

Recommendation: If you want the easiest setup with the most growth potential, Stripe or Square are the industry standards. If you are focused on minimizing processing fees and have higher transaction volumes, investigate Helcim.

Square Invoices is a straightforward option if you’re in the U.S.: it lets you request a deposit and set a separate due date for the remaining balance. You can invoice the balance later or, with the customer’s permission, use a saved card for a later charge. ¹⁰¹²

Stripe is a good alternative if you want more flexibility or already use Stripe. You can collect a deposit, then invoice or charge the remaining amount later; automatic charging requires a saved payment method. ²⁸

For U.S. pricing, Square lists invoice payments at 3.3% + 30¢ on its Free plan; saved-card or manually entered payments are 3.5% + 15¢. Stripe’s standard domestic card processing starts at 2.9% + 30¢, and its Starter invoicing plan adds 0.4% per paid invoice. Rates and features can vary by country and plan. ¹¹⁷

Quick pick: Choose Square for a simple deposit-and-balance invoice workflow; choose Stripe if you need more payment setup flexibility. Get clear customer consent before charging a saved card later.