When you start a PhD you probably expect failed experiments, some long hours in the lab, and a good dose of imposter syndrome. What you don’t expect is that one of the hardest parts might be your relationship with your PhD supervisor.
Sadly, experiencing problems with your PhD supervisor is far more common than prospective PhD students realise. Such problems can range from lack of support to major disputes about research direction, and they can take a heavy toll on your progress and wellbeing. The good news is that most conflicts can be managed if you know how to approach them.
In this post, I’ll walk you through the most common types of problems you may experience with your PhD supervisor and what you can do when things go wrong.
Still selecting your PhD supervisor? Be sure to also check out the related posts below:
- How to Choose a PhD Project & Supervisor
- Signs of a Bad PhD Supervisor: 7 Red Flags to Watch Out For
Why Your Relationship With Your PhD Supervisor Is So Important
Before we delve into the details of the specific types of problems you may face, I’d like to first touch on why the relationship with your PhD supervisor is so important.
In many countries, rather than being called supervisors they’re known as advisors, and for good reason.
Your supervisor isn’t just there to sign documents or suggest papers to read. Ideally, they are a mentor, guide, and advocate for your development. They can influence the conferences you submit your work to, enabling research visits, where your papers are published, and even whether you finish your PhD on time.
But when the relationship is strained with your PhD supervisor, the fallout is significant. A lack of support or ongoing conflict can leave you feeling isolated and stuck. It’s no exaggeration to say that PhD supervisor problems can make or break the entire doctoral experience. I was fortunate during my own PhD but I’ve seen the issues that a poor supervisory relationship can cause.
So let’s now explore some of the most common problems PhD students typically face with their supervisor.
Common PhD Supervisor Relationship Problems
Problem 1: Lack of Input and Support
One of the most frustrating PhD supervisor problems is a lack of engagement. You may send off a carefully prepared draft only to hear nothing for weeks, or receive vague comments back like “needs work” with no real guidance, or find that your supervisor is generally too busy to meet with you. In the meantime, your project stalls because you don’t know what direction to take.
I’ve seen this happen a lot. It is particularly frustrating when every week there is a different (completely foreseeable) excuse.
What to do: If you’re in this situation, it’s important to act quickly. Don’t let months drift by. Make it very clear that you feel their input is important for you to progress the project.
I’d suggest to start by directly asking (over email) for a meeting so that you can talk through the input you need. Hopefully the meeting goes ahead and you can receive some of the required input there and then. In the meeting you can agree on a reasonable plan and timeframe for any future bits of feedback required in the near future, for example committing to reading a paper draft in two weeks’ time.
If the meeting doesn’t happen, chase it up by replying to the same email chain. Hopefully you won’t have to escalate the issue within the university but if you do, having clear evidence of the lack of support will be useful.
Longer term, I suggest setting up regular meetings. Not group meetings with the whole research group, just between you and your supervisor(s). You’ll see this advice regularly throughout my posts, I really do think it is a key step towards a successful PhD. These don’t have to be weekly, but even a short monthly check-in can keep you moving.
I’ve seen people also send short email summaries after meetings to record agreements and next steps. I didn’t bother with this myself but can see how this protects you later if your supervisor claims something different.
Problem 2: Disagreements About Research Direction
Disagreements aren’t always bad—in fact, they can sharpen your ideas. But they become a problem when you feel like your opinion isn’t being listened to. Perhaps you’re passionate about a specific question, only to have it dismissed without explanation. Or maybe your supervisor insists you follow their pet project, even when it doesn’t fit your interests.
I’ve seen this myself where certain academics will have a particular affinity to certain techniques, datasets, or research directions. Sometimes these recommendations are well founded, other times it can be outdated or not applicable to your project.
The shift in expertise during a PhD
Often at the start of the PhD the supervisor will be more knowledgable in the research topic than the PhD student. Hopefully this is the case, otherwise they’re probably not the best supervisor to advise you on the work!
But, as you progress throughout your PhD over time you’ll become more of an expert, so it’ll become common for you to be in a position to question your supervisor’s advice.
A good supervisor will have enough self-awareness to support you throughout this process and not get offended by what a bad supervisor could perceive as you questioning their competence.
I can remember the exact conversation where my supervisor (and a very good one at that!) brought this shift in expertise to my attention with a comment along the lines of: “Jeff, you’re really developing expertise in this area now and raising a lot more questions and suggestions than the start of the PhD”.
What to do: Research direction disagreements are one of the more subtle PhD supervisor problems, because it can feel like you’re not “allowed” to push back. And sometimes the signs of their disagreement can be subtle, such as body language, rather than openly being raised.
Remember though: it’s your PhD. You have the right to question why they’re proposing a particular direction, and to steer the project in the direction you think is best.
A good approach is to ask clarifying questions such as: “Can you explain why this approach might be stronger than the one I suggested?” You can also seek second opinions from co-supervisors or trusted postdocs. Sometimes an outside perspective will confirm that your instincts are sound.
Problem 3: Authorship and Collaboration Conflicts
Few things cause more tension than authorship and collaborations. You might do the bulk of the work, but your supervisor insists on being the first author. Or they insist on one of their collaborators being listed as an author despite them having no input into the paper. Or perhaps you’ve identified a collaborator who could help with your project, but your supervisor refuses because they want full control.
I didn’t experience these problems during my own PhD but have done more recently as a postdoc: where senior academics were trying to add collaborators as authors despite no involvement in the work.
These situations are common and count as serious PhD supervisor problems because they affect not just your current project but your future career prospects. More broadly, misattributing academic credit is at best bad practice and at worst fraud.
Not being first author when you led the work can diminish the visibility of your hard work to future employers. Convention is so strong that authorship order indicates who did what, that Nobel prizes are fairly regularly handed out to the first and last authors of particularly impactful papers.
What to do: To handle this, try to discuss authorship expectations early in the process – ideally before you even begin writing. Keep a record of who contributed what, and don’t be afraid to revisit the conversation if things change.
If your supervisor blocks reasonable collaborations, firstly ask them why they’re opposed to it. You can still build your network by attending seminars, conferences, or even reaching out informally to others in your field. And if disputes become unmanageable, involve your programme director or postgraduate tutor. They’re used to mediating in these situations.
Problem 4: Jeopardising or Delaying Your Thesis Submission
Perhaps the most damaging problem is when a supervisor blocks or delays submission of your PhD thesis. Sometimes this is because they genuinely believe the thesis needs more work. But in other cases, students are held back for less noble reasons – such as providing cheap labour for the lab. Being told “you’re not ready” without clear feedback is particularly destructive.
A few years ago I was in the US for a conference and stopped by the Boston area before returning. While meeting a few potential collaborators at MIT, I met someone whose partner was in about the eighth year of their full-time PhD, and it very much sounded like it was the supervisor (or “advisor” as they’re known in the US) causing the delays.
What to do: If this happens, push for specifics. Ask: “What exactly do I need to improve before submission?” If you don’t get a clear answer, consult your second supervisor or Director of Postgraduate Research.
In many universities, students can submit their thesis without formal supervisor approval, though this can be politically tricky. Knowing the rules at your institution gives you more power to challenge unfair delays.
Problem 5: Unrealistic Workload Expectations
Some supervisors expect total devotion. You might hear comments like “real researchers don’t take holidays” or get emails at midnight with the expectation of an immediate response. They may set impossible publication targets, insisting that a certain number of particularly high-impact first author papers are the minimum for graduation. I expect this was the cause of the delay in the MIT PhD student graduating who I mentioned in the previous section.
A reasonable supervisor will recognise that it is a false economy pushing you too far, and that you should be able to maintain a life outside of the lab. As I mention many times, a PhD is a great period in your life to explore opportunities such as trying new hobbies, making friends, or developing career connections. See my full post about making the most of opportunities for more details.
What to do: This is one of the most toxic PhD supervisor problems, because it can destroy work–life balance and lead to burnout. If this sounds familiar, start by setting boundaries. Decide when you’re available and communicate this clearly. You might say: “I don’t check email after 6pm, but I’ll aim to respond the next day.”
If pressure continues despite reasonable boundaries, escalate to your programme director or graduate tutor. Your wellbeing is not negotiable, and no PhD is worth sacrificing your health for.
Problem 6: Unprofessional or Inappropriate Behaviour
Sometimes the problem isn’t lack of feedback or workload expectations, but behaviour. Maybe your supervisor shouts in meetings, makes inappropriate jokes, or plays favourites in the lab. Even occasional outbursts can be corrosive and lead to a toxic environment and relationship.
What to do: The key here is to trust your instincts. If a comment or behaviour leaves you feeling uncomfortable, it matters. If you feel comfortable, raise it privately with your supervisor. Document what happened with dates and details, even if you never end up using it. That record can be vital if you need to make a complaint later.
Most universities have formal processes for reporting and handling misconduct (such as this example from the University of Bristol), and you don’t have to tolerate disrespectful or unsafe behaviour.
During my own PhD the university offered “active bystander” training, which I attended, to better equip me to know how and when to raise these types of issues. You can see if your university offers something similar. If it doesn’t, you could raise the idea with the graduate school.
How to Maintain a Strong Relationship With Your PhD Supervisor
While not every issue can be prevented, there are steps you can take to reduce the likelihood of encountering problems with your PhD supervisor and keep your relationship strong:
- Set expectations early. Discuss milestones, feedback timelines, and authorship before they become issues.
- Communicate regularly. Even if your supervisor is busy, propose short meetings to stay on track.
- Take ownership. It’s your PhD, don’t wait passively for direction. Propose ideas, take initiative, and drive the project forward.
- Check what’s typical. Talk to other students to see how your experience compares. Sometimes what feels like a huge issue is, unfortunately, normal in your department. Other times, you’ll realise you’re being treated unfairly.
- Document agreements. Written records reduce misunderstandings and provide evidence if conflicts escalate.
What to Do If Things Go Wrong
The first step I’d always suggest is to voice your concerns with your supervisor. More often than not you can then have a productive discussion to address the issue. It is possible that there was a misunderstanding.
However, even with preparation, problems with your PhD supervisor can still arise. If you’re struggling, here are some steps you can take:
- Seek another perspective. Talk to a co-supervisor, postdoc, or senior academic you trust. They can help you decide whether the issue is minor or serious.
- Use university support. Every institution has structures for pastoral care, conflict resolution, or even supervisor changes. Directors of Postgraduate Research and graduate tutors are there to help.
- Build peer support. Talking to other PhD students (both in person and online) can reduce the isolation. Just be careful not to get sucked into endless negativity on forums.
- Keep records. Save emails, note dates of missed deadlines, and document inappropriate behaviour. Hopefully they won’t be required, but these notes will be crucial if you ever do need to escalate formally.
- Protect your wellbeing. Exercise, socialising, and taking breaks are all great ways to gain some perspective on the situation whilst improving your health. For more guidance on protecting your wellbeing during your PhD check out my post on PhD Burnout: Managing Energy, Stress, Anxiety & Your Mental Health. And if your PhD is seriously damaging your health, consider whether staying is worth it. Dropping out is a difficult decision, and isn’t to be taken lightly, but sometimes it’s the healthiest option.
Final Thoughts
Nobody warns you that supervisor conflict may well be the hardest part of your PhD. But knowing how to spot and handle PhD supervisor problems makes a huge difference. And remember that you’re not alone, many PhD students experience the same struggles with maintaining a strong relationship with their supervisor.
And if you’re already in the thick of it, remember: you do have options.
Whether it’s through better communication, university support, or simply protecting your wellbeing, you can take back some control. Your PhD should be challenging for the right reasons – not because of unnecessary problems with your supervisor.
Wish there was a way to know upfront whether your potential PhD supervisor would work out? Be sure to check out the 7 Red Flags to Watch Out For.
Do you have any suggestions for maintaining a strong relationship with your PhD supervisor? Share them in the comments!
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