If a supervisor has ever handed your methodology chapter back with "this needs more justification" scrawled in the margin, you're in good company. It's the single most re-drafted chapter in a thesis, and almost always for the same handful of reasons.
1. The method doesn't visibly answer the research question
A methodology chapter isn't a neutral description of what you did, it's an argument that your chosen approach is the right tool for your specific research question. If a reader can't trace a direct line from your research questions to your method choice, that gap is the first thing a supervisor will flag.
The fix is usually structural, not content: open the chapter by restating your research questions, then explicitly justify each major methodological decision against them, rather than burying that justification in a literature summary.
2. Limitations are mentioned, not engaged with
Every method has trade offs, and reviewers know it. Naming a limitation in a single sentence without discussing how you mitigated it, or why it is an acceptable trade off, reads as an afterthought rather than a considered decision.
A methodology chapter that anticipates its own weaknesses is far more convincing than one that pretends they don't exist.
3. Sample size or data source justification is missing
"We surveyed 150 participants" is a fact. "150 participants was determined using G*Power at 0.8 power for a medium effect size, consistent with similar studies in this field" is a justification. The second version is what gets chapters approved.
4. The analysis plan is described after the fact, not before
A common giveaway that an analysis plan wasn't pre registered or thought through in advance is when it reads as a description of what happened, rather than a specification written before data collection. Where possible, frame your analysis plan prospectively, even in the write up.
A quick self check before you submit
- Does every methodological choice trace back to a specific research question?
- Have you named at least one limitation and how you addressed it?
- Is your sample size or data source justified with a number or a citation, not just stated?
- Would a reader unfamiliar with your field understand why you chose this method over the alternatives?
Where this fits into the bigger picture
Methodology chapters rarely fail because the underlying research is weak, they fail because the justification wasn't made visible on the page. That's a writing and structuring problem, which means it's fixable without redoing your research.
If you want a second pair of eyes on your own methodology chapter before it goes back to your supervisor, that's exactly the kind of review our thesis and dissertation support covers.