Quick answer

QuickBooks Time payroll sync problems are usually not connection failures. In QuickBooks Online Payroll and QuickBooks Desktop Payroll, only approved timesheets export, and each employee must be mapped to a payroll item. Check the approval status, the pay-period closing date, and the payroll mapping before you touch the connection, then re-authorize the integration only if hours still do not move.

What "QuickBooks Time not syncing with payroll" actually means

QuickBooks Time records and approves hours; QuickBooks Online Payroll or QuickBooks Desktop Payroll turns them into paychecks. A payroll sync problem means the handoff between the two broke, not that the hours were lost.

With QuickBooks Online Payroll, approved time becomes available to the pay run with no manual export. With QuickBooks Desktop Payroll, approved time exports into the weekly timesheet during Employees → Enter Time → Sync QuickBooks Time. One rule applies to both: only approved timesheets move.

QuickBooks Time also never exports pay rates to QuickBooks Desktop, only approved hours and payroll items. If a rate looks wrong in the paycheck, the problem is in the Desktop employee record, not the sync.

Symptoms of a payroll sync problem

  • Hours are visible in QuickBooks Time, but the pay run preview or weekly timesheet shows zero or last period's numbers.
  • Some employees export and others do not, even though everyone tracked time.
  • A Desktop sync finishes with no error, yet the weekly timesheet stays empty.
  • Hours appear twice after a re-sync or after someone edited time that had already exported.
  • Overtime arrives as regular pay, or time off hours are missing.

Common causes, ranked by how often they occur

  1. The timesheets were never approved. Unapproved or rejected time simply sits in QuickBooks Time and never reaches payroll.
  2. Time was edited after it exported. Approved and exported time locks; corrections do not flow until you unapprove or unlock the original entry.
  3. Payroll items are not mapped. In QuickBooks Desktop, each employee needs at least one payroll item mapped before any time can export.
  4. The pay period or closing date is wrong. If the closing date sits after the hours, the current period pulls in nothing.
  5. Employee records do not match. A new hire may exist in payroll but not in QuickBooks Time, or lack the setting that lets Desktop payroll use time data.
  6. A required field is blocking the timesheet. A required customer, service item, or custom field with nothing assigned stops that employee from finishing the timesheet.
  7. The integration connection broke. A removed add-on, renamed company file, moved server, expired sign-in, or wrong Intuit account stops the export quietly.

Before you begin

  • Sign in to QuickBooks Time as an administrator; only admins can change company settings and payroll mapping.
  • Note the pay period you are processing and the last date that actually exported.
  • If you are changing QuickBooks Desktop payroll preferences, back up the company file with File → Back Up Company → Create Local Backup.
  • Allow 20 to 30 minutes for approval and mapping fixes; reconnecting a Desktop integration takes longer.

Do not unlock or unapprove time that has already been paid. Unlocking exported time removes the lock from hours that may be on a filed payroll run, and re-syncing can create duplicates. Confirm with your payroll administrator before changing any processed period.

How to fix QuickBooks Time not syncing with payroll

1

Confirm which integration you are running

In QuickBooks Online, go to All apps → Time → Overview; if the page offers Go to Classic QuickBooks Time, you have the full Time account and can approve in either place. In QuickBooks Desktop, look for Use QuickBooks Time or Sync QuickBooks Time under Employees → Enter Time. If those options are missing, the add-on is not connected on this computer, which is often the whole problem.

2

Approve the timesheets that are missing from payroll

In QuickBooks Online, go to All apps → Time → Approvals, filter the status to Unapproved, then select Approve and Approve and lock time. In classic QuickBooks Time, open Approvals, choose your dates and team members, select Run Report, then Select all unapproved and Approve Selected. Approving locks the displayed hours. If your team uses timesheet submissions or DCAA compliance, approve in classic QuickBooks Time instead of QuickBooks Online.

Corrections only. The next step is for hours edited after they exported. If the hours have not been paid yet, unlock only the affected employee and dates, not the whole company.

3

Unlock and re-approve time that was edited after export

If payroll still shows an old number, the entry is still locked. In classic QuickBooks Time, open the QuickBooks dropdown and select Unlock Exported Time, choose the dates and employees, then select Unlock Timesheets and confirm. Unlocking is limited to the past 90 days. If the time has not exported yet, use Approvals → Unapprove instead, correct the entry, then approve and lock it again so it exports once, cleanly.

4

Check the pay schedule, closing date, and week start

In QuickBooks Time, go to Company Settings → Payroll & Overtime → Pay Schedule and confirm the schedule matches how you actually run payroll, then pick a recent closing date that puts the current hours inside the open period. Next, align the week start everywhere: Settings → Account and settings → Time in QuickBooks Online, Edit → Preferences → Time & Expenses → Company Preferences in QuickBooks Desktop, and the same Payroll & Overtime area in QuickBooks Time. A Sunday start in one system and a Monday start in another shifts hours across period boundaries.

5

Map payroll items to time types

In QuickBooks Time, open the QuickBooks sync menu, select Preferences, then Payroll Item Mapping Tool. On the Map Employees tab, select an employee and choose the matching pay type for each time type; selections save automatically. QuickBooks Online Payroll maps items on its own, but review the mapping when hours land under the wrong pay type. With QuickBooks Desktop Payroll, mapping is mandatory, so repeat this for every employee, including salaried staff and anyone who works overtime.

6

Match the employee records between the two systems

New employees added to QuickBooks Online are added to QuickBooks Time automatically when the two are integrated; confirm they appear in My Team and have access. If your company is not integrated, add and invite them from My Team → Add team members. In QuickBooks Desktop, open Employees → Employee Center, select the employee, open Payroll Info, and confirm Use time data to create paychecks is selected. Set matching pay rates in both systems, because QuickBooks Time does not export rates.

7

Re-authorize the connection

In QuickBooks Desktop, open the file as admin in single-user mode, go to Employees → Enter Time, select Activate QuickBooks Time, then Sign in with your QuickBooks Time credentials. In QuickBooks Time, open the QuickBooks sync menu, select Preferences, and turn on Export Approved Timesheets when Syncing. If the file previously used the Web Connector, remove QB Time.qwc from the Web Connector, remove QuickBooks Time Integration under Edit → Preferences → Integrated Applications, uninstall the add-on under Feature Add-ons → Manage Add-ons, then reconnect. For a QuickBooks Online company, confirm you are signed in with the Intuit account that owns the company and recheck the sync menu preferences and import options.

8

Run the sync and check for duplicates

In QuickBooks Desktop, select Employees → Enter Time → Sync QuickBooks Time. The sync imports updated customers and items, then exports newly approved timesheets into the weekly timesheet. If you reconnected to fix one employee, verify that paycheck preview before syncing the rest of the company. If hours appear twice, remove the duplicate row on the weekly timesheet, or unlock the time, correct it, and sync once more. Do not sync repeatedly hoping duplicates clear; each pass can add another copy.

Verify the fix

  1. Approve one small correction and confirm it reaches payroll in the pay run preview or the synced weekly timesheet.
  2. Compare per-employee totals for the period in the QuickBooks Time payroll report against payroll; they should match to the minute.
  3. Confirm each line sits under the correct payroll item, including overtime and time off.
  4. Check one employee who previously failed to export, not just the one you tested.
  5. Note the period end date that exported so the next sync has a clear start.

If the problem persists

A few conditions block a sync in ways these steps cannot fix. A required custom field assigned to a team member with no items prevents clock-out or timesheet edits until items are assigned. One QuickBooks Time account can connect to only one QuickBooks Desktop company file. Files created between 2017 and 2020 use the Web Connector, while files from 2021 or later use the built-in integration.

Connection errors after a sync attempt are covered in the QuickBooks Time payroll update error guide. If hours export but the check run fails, move to direct deposit troubleshooting. For payroll-level problems unrelated to time tracking, start with QuickBooks Online Payroll issues. If nothing exports after a full re-authorization, contact Intuit support with the exact period, employee names, and error text, and do not delete timesheets to force a clean slate.

Prevention

  • Approve time daily or weekly, and never run payroll on unapproved hours.
  • Approve and lock the pay period once payroll is final so late edits cannot creep in.
  • Confirm every new payroll employee appears in QuickBooks Time with a mapped payroll item before their first shift.
  • Recheck week start, pay schedule, and mapping whenever a new payroll admin takes over.
  • Keep the Desktop integration on the server and record which Intuit account owns it.

Frequently asked questions

Do timesheets have to be approved before they sync to payroll?

Yes. QuickBooks Time exports approved time only. If an employee tracked 40 hours but the timesheet is still waiting for approval, payroll sees nothing. Approve and lock the time, and it becomes available to the pay run or the next Desktop sync.

Why do exported hours arrive with a zero rate in QuickBooks Desktop Payroll?

Because QuickBooks Time exports payroll items, not pay rates. The rate comes from the employee's payroll record in QuickBooks Desktop. Confirm Use time data to create paychecks is selected under Payroll Info and the rate matches what you use in QuickBooks Time.

Can I edit time after payroll already imported it?

Only after you unlock it. Unapprove the entry if it has not exported, or use Unlock Exported Time if it has; unlocking is limited to the past 90 days. Review any change to a paid period with your payroll administrator first, because it can affect filings and create duplicate hours.

Why did only some employees' hours sync?

Check those employees in order: approval status, payroll item mapping, the Use time data to create paychecks setting, and any required customer, service item, or custom field with nothing assigned. One unapproved or unmapped employee does not block the others, which makes the problem look random.

Does QuickBooks Time work with QuickBooks Desktop Payroll?

Yes. QuickBooks Time Premium or Elite connects to QuickBooks Desktop Pro Plus or Premier Plus and exports approved time into the weekly timesheet. One Time account links to one company file, with the built-in integration for 2021+ files and the Web Connector for older ones. Keep the pay run current with payroll tax table updates.

Sources & further reading