💡 Looking to submit an off-cycle payroll run? Go to the Run off-cycle payroll in Workstream article!
This article walks you through how to run a regular payroll in Workstream from start to finish. You have two (2) options to choose from:
Upload team hours using a spreadsheet - Use this method if you track time outside Workstream and want to upload worked hours, time off, or earnings using a file.
Pull hours from Workstream - Use this option if you're already tracking hours and time off using Workstream’s Time & Scheduling and Time Off products.
Aside from these options, you also have the capability to do everything manually:
Manually enter hours - Use this option if your team tracks hours outside Workstream and you’d rather type them in directly instead of uploading a file. You can also use this option to add or adjust hours on top of what’s already in the payroll draft.
Once the hours are in, you’ll review the payroll totals and check for accuracy. After that, you can make any changes and submit the payroll for processing.
📌 Access needed: To run payroll and download reports, you need the Payroll management permission enabled. If you don't have access, reach out to your Super Admin.
To start a regular payroll run, go to Team View > Payroll > Upcoming tab > Run payroll.
Option 1: Upload team hours using a spreadsheet
💡 Use this option if:
You track hours in a POS, Excel sheet, or other time tool
You want to upload a file with worked hours and/or time off
You’re not using Workstream’s Time Off or Time & Scheduling features
Run payroll
Access payroll
Go to Payroll, then select the Upcoming tab.
Select Run payroll next to the pay period you want to process.
Run payroll
Payroll name (optional): Give this payroll a name. Helpful if you run multiple payrolls within the same pay period.
How would you like to enter your team's hours: Choose Upload your team's hours.
Advanced settings: Leave both boxes unchecked if your file already includes hours and time off.
Apply time off taken from Workstream
Pulls approved PTO, vacation, or sick leave hours from Workstream’s Time Off product.
Apply time entries approved from Workstream
Pulls clock-in/out data from Workstream’s Time & Scheduling product.
Select Next to proceed. If you see a Blocked employees window, go to the Resolve blocked team members article to help resolve this.
Upload your file (import hours)
Upload your team’s hours and time-off data using a spreadsheet. This pulls all your information into the payroll draft.
⚠️ You can’t upload contractors using a spreadsheet. To include them, manually enter their hours.
Here are the accepted file types:
.xlsx (Excel spreadsheet)
.csv (Comma-separated values)
We recommend using the Workstream template to prevent formatting errors.
You have 2 options to choose from:
Upload your file
Select the ➕ plus button to choose a file from your computer, or
Drag and drop a file directly into the upload window
Use the Workstream template (recommended)
The template matches Workstream’s payroll system so there's no need to reformat columns or adjust field names. Here's how to use it:
Select the Download Excel template button to get a ready-to-use file with all the fields Workstream supports.
Prepare your file:
Fill in the key fields (first and last name, job, total hours worked, and any time off or bonuses)
Tooltips in each column explain what to enter
Leave the rest blank if they don’t apply to your setup
Save the file on your computer.
Upload the file using the ➕ plus button or drag it into the upload window.
Map your data
Once uploaded, you’ll land on the Map columns window. This is where you match your file’s data to Workstream’s payroll fields.
📌 If you used the Workstream template and didn’t rename the columns, most fields will map automatically. But always review and confirm.
💡 Things to remember when mapping data
Reimbursements: If an employee doesn’t have a reimbursement, leave the cell blank. Entering 0 will cause an error during the preview step.
Earning amounts: If your file includes both hours and a total amount (for example, 8 hours and $1,200), Workstream will calculate the hourly rate as Amount ÷ Hours.
If you only include hours, Workstream will use the team member's job rate in Workstream.Multiple rows for a team member: If you upload several rows for the same person (for example, across locations or jobs), Workstream will treat each one as a separate earning, which helps for tracking and reporting.
What you're seeing
Uploaded columns: Your file’s headers
Sample data: Preview of what’s in each column
Destination columns: Dropdowns where you choose what each column should map to (like First name, Job name, Hours worked)
What you need to do
Review each row in the table, and use the dropdowns under Destination columns to assign them to the right payroll fields.
Delete rows you don’t need using the 🗑️ trash icon
Select Next to go to the Review & finalize page.
Review and finalize your data
On this screen, you’ll see a full table of the data you’re about to import into payroll. You can also spot and fix any issues before continuing.
What you're seeing
All rows: All your uploaded data
Clean rows: Ready for import
Rows with issues: Needs fixing (like missing fields, invalid numbers)
Find and replace: Lets you quickly edit fields across all rows
Export options: Lets you download your data as Excel or CSV (you can export all rows, or just rows with errors)
What you need to do
Check the Rows with issues tab. Make sure nothing is missing or incorrectly formatted.
Use the Find and replace tool. This is helpful if you need to bulk update a specific value across the spreadsheet.
If everything looks good, select Import. This pulls your mapped and reviewed data into the payroll draft.
💡 Nothing gets finalized or sent to the bank yet. You’ll still review everything before submitting payroll. Review your payroll draft and make your changes before submitting!
Option 2: Pull hours from Workstream
💡 Use this option if you're already tracking hours and time off using Workstream’s Time & Scheduling and Time Off products.
This setup allows Workstream to automatically pull in approved hours and PTO for the current pay period, no uploads or manual entry needed.
Run payroll
Access payroll
Go to Payroll, then select the Upcoming tab.
Select Run payroll next to the pay period you want to process.
Run payroll
Payroll name (optional): Give this payroll a name. Helpful if you run multiple payrolls within the same pay period.
How would you like to enter your team's hours: Choose Manually enter your team's hours.
Advanced settings: Check the following
Apply time off taken from Workstream
Automatically pulls approved PTO, vacation, and sick leave from Workstream’s Time Off product.
Apply time entries approved from Workstream
Automatically pulls approved clock-in/out hours from the Time & Scheduling product. Workstream only pulls hours from the current pay period. It won’t carry over entries from past periods.
Select Next to proceed. If you see a Blocked employees window, go to the Resolve blocked team members article to help resolve this.
Review pulled hours
Workstream will show all pulled hours from approved shifts and time off for the current pay period.
You won’t need to do anything if all the info looks correct. You can go ahead and review all the details and submit your payroll draft.
You only need to manually enter or update hours if:
Some hours are missing or incorrect
Some team members aren’t using Time & Scheduling
Time off wasn’t approved before you started payroll
FAQs: Running a Regular payroll
Q: When should I submit payroll to ensure employees are paid on time?
A: Submission deadlines depend on your payroll processing time:
2-day processing → Submit at least 2 business days before payday
3-day processing → Submit at least 3 business days before payday
4-day processing → Submit at least 4 business days before payday
Where to check your deadline
Inside the payroll draft - Open your draft and check the Payroll summary section:
From the Payroll tab - Go to the Upcoming or Drafts tab to view a table showing the Approval deadline for each pay period:
Q: When are payroll funds pulled from my bank?
A: Workstream now pulls payroll funds on the same day you submit payroll, not the next day. That means once you click “Submit Payroll”, the funds begin processing immediately.
If you submit payroll BEFORE your processing deadline, we debit funds at 7am on the processing date.
If you submit payroll ON your processing deadline, we debit funds approx. 60 minutes after submission.
Q: When do employees get paid?
A: Employees are paid on your scheduled payday, as long as you finalize and submit payroll by your processing deadline. For example, if you're on a 2-day processing schedule, you’ll need to submit payroll by Wednesday for a Friday payday.
Q: How do I know if I submitted payroll correctly?
A: Once you finalize payroll, your draft will lock and show in the "Submitted" tab in Payroll. You’ll also get a confirmation email. If you’re unsure, go back into the Payroll tab to double-check. Unsubmitted drafts are still editable. Keep in mind that employees will not get paid if a payroll is in draft.
Q: What should I do if I miss the payroll deadline?
A: If you don’t submit payroll by the deadline, Workstream can't automatically process it for you. You have a few options depending on timing:
Manual payment: You can pay team members directly by check, cash, or another method outside of Workstream. To calculate the correct net pay and withholdings, run a manual payroll in Workstream before making the payment. This ensures your records and tax filings stay accurate.
Next Day Pay: If your company uses 2-day processing and you catch the mistake before payday, you may be able to switch the run to Next Day Pay. This depends on cutoff timing and may not always be possible.
Contact support: If you missed the deadline and can’t make a manual payment, reach out to our support team as soon as possible. We’ll check if there are any available options based on your payroll processing setup.
Q: Can salaried employees be paid through Workstream Payroll?
A: Yes, you can pay salaried employees in a couple of ways:
Through T&A import – Just include their hours in a column labeled "Salaried Hours". As a best practice, enter standard hours based on the pay frequency for salaried earnings:
Weekly: 40
Bi-weekly: 80
Semimonthly 86.67
Monthly 173.33
Quarterly: 520
Annually: 2080
Manually in the payroll draft – You can enter their hours and details directly before processing payroll
Q: Are there any extra fees I should know about when running payroll?
A: Certain payroll actions may come with additional fees. To understand when these fees apply, it’s best to review the full list before processing payroll.
Q: Can Workstream offer Next Day Pay?
A: Yes! It’s an optional feature that lets you submit payroll just one business day before payday, instead of two.
Available only to customers on 2-day processing
Must submit by 5 PM PT the day before payday
Pricing: $1 per employee per month
This can be adjusted when submitting your payroll draft:
Q: What steps should I take if I need to reverse a payroll payment?
A: If you need to reverse an ACH payroll payment, contact support as soon as possible so we can help. Reversals must be submitted within five banking days after the funds have settled. After that, they can’t be processed.
Reversals are only allowed in these cases:
Duplicate payment
Incorrect payment amount
Incorrect recipient or account number
A final paycheck was already issued by check, but the ACH payment still went through, resulting in a duplicate payment
Keep in mind that partial amount reversals are not allowed.