QB Issue Resolution:
Yes, you’ll have to continue paying for the employer portion of the Social Security and continue deducting the employee portion from his pay.
The wage base limit is independent per employer. If your employee has reached the limit and paid the SS in excess because he has two employers, he can request for a refund. He can reach out to a tax advisor to recover the excess.
Resolution for Issue 'Stop Social Security Deduction for employee with income from another employer' available: Yes (Solved).
Source: Intuit Community forum.
Stop Social Security Deduction for employee with income from another employer: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.Support for base limit
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Error Recovery for base limit [Canada]
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