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Handling Employee Complaints Against a Manager
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How to Handle Employee Complaints About a Manager: A C-Suite Guide

By Kellie Rondon on Jul 07, 2025
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Even in the most collaborative workplace cultures, leadership missteps happen. For business owners and executives, employee complaints about a manager can feel like walking a tightrope: ignore the issue and risk legal liability or cultural fallout; overcorrect and risk undermining a valued leader. Either way, how you respond matters.

Handled properly, these situations become an opportunity to reinforce a culture of accountability, fairness and trust. Handled poorly, they can damage morale, spark turnover and erode your company's reputation.

This guide offers a clear framework for executives who want to do more than just "check the box" on investigations.

RELATED: Retaliation Claims - Why There's Never a Good Time to Get Even >>

Step 1: Take Every Complaint Seriously—Without Jumping to Conclusions

Start by making space for the employee to speak in a private setting. Thank them for coming forward, and listen closely without promising a specific outcome. The tone set in this initial conversation is critical. Employees need to know their concerns are taken seriously, even if you later determine no policy was violated.

What you don't want to do:

  • Dismiss the complaint outright

  • Downplay the employee’s experience

  • Assume the manager’s performance outweighs the concern

Letting performance shield problematic behavior creates risk on two fronts: employee disengagement and potential legal exposure if the conduct later escalates.

Depending on the nature of the complaint, you may need to take immediate steps to protect the employee from further harm. For serious allegations—like harassment, discrimination or retaliation—consider:

  • Temporary reporting structure changes

  • Remote work accommodations

  • Administrative leave for the accused while the matter is reviewed

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Step 2: Launch a Fair, Confidential and Well-Documented Investigation

Once a complaint is raised, the process must move swiftly and thoughtfully. Begin by identifying who will lead the investigation. In some cases, this can be handled internally by your HR team. In others—especially if the complaint is about someone in HR or a member of senior leadership—you may want to bring in a neutral third party.

Getting to the “bottom” of an employee complaint against a manager is never easy—it can be a game of “he said, she said” that leaves the business wondering what action to take.

When the accused and accuser tell completely different stories:

  • Ask the complaining employee if anyone else can corroborate their account

  • Interview the manager’s other employees to identify potential patterns

Tangible proof of misconduct seems like an obvious item to bring to a meeting to discuss a complaint, but many employees don’t think to mine their files for evidence. Ask the accuser if they have:

  • Emails

  • Voicemails

  • Instant messages or other written records

As you’re digging into the details of what happened, make sure to document every bit of information you come across. In the event the complaining employee takes the matter outside of the company, having clear documentation of your investigation will be of utmost importance.

Memories fail and circumstances can change. Clear documentation on file substantiates the decisions and actions that were taken as a result of the investigation.

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Step 3: Make a Decision and Take Consistent, Proportionate Action

After reviewing all available evidence, determine whether the complaint is substantiated and if a policy or behavioral expectation was violated. Then, decide what action to take.

Consistency matters. Avoid:

  • Over-disciplining one manager while excusing another for similar behavior

  • Allowing past performance or popularity to influence outcomes

Discipline doesn't always mean termination. Depending on the findings, appropriate responses may include:

  • Coaching

  • Additional training

  • Formal warnings

  • Reassignment or leadership changes when necessary

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Step 4: Strengthen Your Culture and Reporting Processes

Every employee complaint—substantiated or not—provides insight into how your workplace operates. Use the experience to evaluate and improve your policies, training and communication.

Ask yourself:

  • Do employees have multiple ways to safely report a concern?

  • Are managers trained to recognize and prevent retaliation?

  • Are your behavioral expectations clear and consistently enforced?

For small businesses without a full in-house HR team, one of the most impactful changes you can make is working with a certified professional employer organization (PEO).

Axcet HR Solutions helps business leaders navigate complex employee relations issues with confidence and compliance. From neutral investigations to manager training and policy support, our certified HR consultants are just a call away.

Turning Complaints Into Opportunities

When an employee brings forward a complaint about a manager, it can feel like a threat to team harmony. But handled well, it becomes a chance to show that your company values fairness, integrity and accountability at every level.

That’s leadership your employees will respect—and your culture will reflect.

RELATED: What is a PEO and How Can it Help Your Business? >>

Don’t Leave Employee Complaints to Chance

When it comes to legal risk and company reputation, the stakes are too high. Let Axcet’s certified HR professionals help you respond decisively—and in line with your values. Schedule a time to speak with our experienced team today >>

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