If you’re running payroll in QuickBooks and still writing out checks or making manual payments, setting up Direct Deposit is a simple upgrade that saves you time, reduces paper clutter, and ensures your team gets paid faster. Whether you’re new to QuickBooks Payroll or just haven’t gotten around to turning this on, now’s a good time to do it. Let’s walk through how to get it set up from start to finish, no complicated tech talk.
Step 1: Check Your Payroll Subscription
Before jumping in, make sure you’re signed up for a QuickBooks Payroll plan that includes Direct Deposit. Most QuickBooks Online Payroll and QuickBooks Desktop Payroll services support it, but you’ll want to double-check.
You can do this by going to:
- Gear icon > Account and Settings > Billing & Subscription (in QuickBooks Online),
or - Employees > My Payroll Service > Account/Billing Information (in Desktop).
If you’re good to go, move on to the setup.
Read Also: How to Pay myself in QuickBooks
Step 2: Add Your Business Bank Info
QuickBooks needs a bank account to pull payroll funds from. Here’s how to connect it:
In QuickBooks Online:
- Go to Payroll in the left-hand menu
- Click on Overview, then choose Setup direct deposit
- Enter your company’s bank account details (routing number, account number, account type)
- Intuit will deposit two small test transactions within 1–2 business days
- Once they show up in your bank account, return to QuickBooks to verify the amounts
In QuickBooks Desktop:
- Click Employees > My Payroll Service > Activate Direct Deposit
- Follow the prompts to enter your business’s bank info
- Just like with Online, you’ll receive two small test deposits for verification
Don’t skip this step, it’s how QuickBooks confirms it’s really your account.
Step 3: SetUp Direct Deposit for Each Employee
Once your company info is verified, you can start enrolling employees:
In QuickBooks Online:
- Go to Payroll > Employees
- Select the employee you want to set up
- Click Edit in the “Pay” section
- Turn on Direct Deposit
- Enter their bank account number, routing number, account type, and choose whether to deposit the full amount or split between multiple accounts
In QuickBooks Desktop:
- Go to Employees > Employee Center
- Double-click the employee’s name
- Choose Payroll Info, then click Direct Deposit
- Check “Use Direct Deposit for this employee”
- Enter their bank info and save
You’ll want to collect a voided check or bank letter from each employee to avoid typos or mismatches.
Step 4: Run Payroll and Use Direct Deposit
Once everything’s in place, your next payroll run can go through Direct Deposit, just like that.
- In QuickBooks Online, go to Payroll > Run Payroll, select the pay period and employees, and confirm Direct Deposit is turned on.
- In QuickBooks Desktop, go to Employees > Pay Employees, select your payroll schedule, and make sure Direct Deposit is enabled when reviewing paychecks.
Payments typically take 2 banking days, but you can opt for same-day direct deposit if your plan supports it.
Step 5: Confirm Paystubs and Let Employees Know
QuickBooks will automatically generate paystubs. You can:
- Email them to employees
- Allow access through the Workforce portal (for QuickBooks Online Payroll users)
- Or print physical copies, if needed
A heads-up to your team is always a good idea, especially the first time. Let them know when to expect the deposit and how to check their stub.
Extra Tips to Keep in Mind
- Cutoff Times Matter: For most QuickBooks Payroll accounts, you’ll need to run payroll by 5 PM PT at least 2 banking days before payday.
- Bank Holidays: Remember, weekends and holidays can delay transfers.
- Split Deposits: Employees can choose to split their pay check between checking and savings accounts, which helps with budgeting.
To Conclude
Setting up Direct Deposit in QuickBooks really only takes a few steps, and once it’s done, you won’t miss the old way. No printing checks. No last-minute runs to the bank. Just a few clicks, and your employees are paid on time, every time.
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