Direct Deposit

How direct deposit works for small business payroll

Direct deposit sends wages from your business bank account to your employee’s bank account through the ACH (automated clearing house) network. It’s a less time-consuming way to pay employees, skipping paper checks and trips to the bank. Once you set it up, you can run it on schedule every time.

Setting up direct deposit for your small business means making a short list of decisions. Here's what direct deposit setup looks like: how ACH works, what to collect from each employee, the full sequence, and how to resolve a failed deposit.

SurePayroll By Paychex automates direct deposit for your team from setup to deposit, on your schedule.

How ACH functions when you run direct deposit payroll

ACH is the network that processes every direct deposit you run. When you initiate a payment, you send instructions through the Automated Clearing House network to each employee’s bank. Those instructions specify the amount to deposit, the account to credit, and the date funds should arrive.

Standard ACH processing takes one to two business days for regular payroll runs. Initiate two days before payday. Submit Wednesday and employees receive their pay on Friday.

Same-day ACH processes deposits the same business day, provided you initiate before the daily cutoff. It typically costs more per transaction. Use same-day direct deposit for corrections or off-cycle payments.

What to gather before setting up direct deposit

Have this information in hand before you process your first direct deposit payroll.

From each employee: Routing number (the nine-digit number that identifies their bank), account number, and account type (checking or savings). You’ll also need a signed direct deposit authorization form before their first electronic payment. Most employees find their routing and account number through their online banking app or on a paper check.

On your end: A business bank account enabled for ACH transfers. Confirm this with your bank before you start. You also need a payroll system or a direct arrangement with your bank to originate ACH files. For your small team, you can outsource an online payroll service or direct deposit processing.

Optional but worth requesting: A voided check or bank letter from each employee. It gives you a verified record of routing and account numbers before the first deposit and catches typos before payday.

SurePayroll walks you through what to collect and where to enter it.

How to collect and file direct deposit authorization  forms

Get a signed authorization form from every employee before their first direct deposit. It documents that they chose electronic payment and provided their banking information. This is your record and your employee’s record that you executed payroll according to the details they provided

A complete authorization form captures the banking information you collected, plus employee name, bank name, signature, and date. Keep signed authorizations in your payroll records, secured and organized. If an employee changes banks, get a new signed authorization before updating their banking information in your payroll system.  

Your state may shape what that form looks like and whether direct deposit is even mandatory. State rules vary on mandatory direct deposit. Some states require you to offer paper checks as an alternative, and some require specific consent language on the authorization form. Check your state’s wage payment laws before requiring direct deposit.  

Employees can revoke authorization at any time, typically with written notice.

How to set up direct deposit for your team

Setup follows a step-by-step process: collect authorizations, enter banking information, verify accounts, and process your first payroll.

Give employees two to four weeks’ notice before moving from payroll from paper checks to direct deposit. Explain what employee information you’ll need and what they can expect on their first payday.

Collect employee banking information

Distribute authorization forms and give employees one to two weeks to return them with routing number, account number, account type, and signature. Request a voided check or bank letter along with the form if you want additional verification before entering their banking information.

Enter information into your payroll system

Once you have signed authorizations, enter each employee’s banking information into your payroll system. Double-check routing and account numbers before saving.  

Run a test deposit

A small test deposit of one dollar or less confirms the account is active and the numbers are correct. If it goes through, the account details are valid. If it fails, you catch the error before payday. Run one for any new employee whose account details you cannot verify with a voided check.

Submit your first payroll

Enter employee hours, review gross pay, and submit at least two business days before payday. Most online payroll systems automate direct deposit once you enter employee banking information.  

SurePayroll calculates net pay, initiates the ACH transfer, on the schedule you set. You submit payroll. The system processes deposits on your schedule. After initial setup, direct deposit runs with each payroll automatically.

Confirm deposits arrived

On payday, verify that deposits processed successfully. If any deposit fails, fix it the same day.

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How to handle direct deposit for employees and contractors

Direct deposit works for both employees and independent contractors whether you pay them weekly, biweekly, semimonthly, or monthly.

The ACH setup process is identical. You’ll need their routing number, account number, authorization form, electronic transfer. The difference is how you treat taxes.

Employees have federal and state income taxes, Social Security, and Medicare withheld from gross pay. Independent contractors receive the full payment amount without tax deductions. They’re responsible for their own tax filing and estimated payments to the IRS.

Keep separate authorization forms for employees and independent contractors, even though the payment process is the same. It clarifies the working relationship and keeps your payroll data accurate. This separation means the right year-end forms generate automatically in January.

Year-end forms differ for each worker type. Employees receive W-2 forms showing wages and withholdings. Contractors paid $2,000 or more in 2026 receive 1099-NEC forms showing total payments. That threshold is set to index for inflation in 2027. If you pay both through the same payroll software, it tracks payment types separately and generates the correct year-end forms automatically.

Causes and fixes for a failed deposit

A failed deposit needs same-day attention. When an ACH transfer is rejected, your bank sends a notification, usually within one or two business days. Your employee will not receive the deposit on payday.

Failed deposits trace back to five causes. Here is what to check and how to fix each one.

Routing number error

The ACH network rejects the transfer before it reaches the employee's bank. Verify the routing number directly with the employee using a voided check or bank letter, correct it, and resubmit. Most banks let you run an off-cycle payment the same day.

Wrong account number

The routing number is valid but the account does not exist at that bank. Contact the employee, get verified account details, update the information, and resubmit. Use same-day ACH if it's available to get payment to the employee quickly.

Closed account

Your employee changed banks without notifying you. Request updated banking information and a new signed authorization. Issue a paper check while you wait. Switch back to direct deposit once you have verified details on file.

Account type restriction

Some savings accounts block incoming ACH deposits. Ask the employee to provide a checking account instead.

Insufficient funds

Your cashflow needs to cover total net pay before submitting payroll. If your business bank account is short, every deposit fails at once. Your bank may charge NSF fees. Fund the account, resubmit the full payroll run, and confirm your balance before each payroll period with enough buffer to cover total net pay.

How to fix it fast

Tell your employee what happened and when to expect payment. Most payroll systems let you run an off-cycle payment to resubmit failed deposits without waiting for the next regular payroll run. If same-day ACH is available, use it.

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Direct deposit built for your business

SurePayroll automates direct deposit for your team: setup, tax calculations, ACH processing. You enter employee banking information once. Submit payroll each period. The system handles the rest on your schedule, so nothing slows you down.  

See how SurePayroll works

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