Your methodology section is not a checklist. It’s not a procedural rundown of what you did. And it’s certainly not the least important part of your paper.
Yet most researchers treat it exactly that way. Describe the method. Move on. The result? Rejection letters citing “methodological concerns” and the frustrating reality that your solid research gets questioned because you never showed editors that you understand your own approach.
The Real Problem: Why Editors Scrutinize Methodology So Intensely
When editors read a vague, incomplete, or poorly justified methodology section, they’re asking a single question: does this researcher actually know what they’re doing?
The answer determines everything. It determines whether your findings are credible. It determines whether your work is reproducible. It determines whether you’re a researcher who thinks carefully about their choices or someone who just went through the motions.
Pain Point 1: The Checkbox Mentality
Many researchers genuinely believe the methodology section exists to describe what happened. You conducted interviews. You analyzed data. You used software. Report it and move on.
But this approach creates a critical problem: it reveals nothing about your thinking. When you write “We conducted 20 semi-structured interviews,” you’ve answered what, not why. Editors immediately wonder: Why 20? How did you decide that number? What would you have missed with 15? What problems emerge with 25?
Your silence on these questions signals one of two things: either you didn’t think through your methodological choices, or you don’t understand them well enough to defend them. Both are rejection-worthy.
The researcher with a checkbox mentality treats methodology as obligation. The researcher who understands methodology treats it as the foundation of credibility. When editors encounter the first approach, they doubt everything that follows.
Pain Point 2: Hidden Limitations and Undefended Assumptions
Every methodology has constraints. You chose one data collection method over another. You selected a specific sample. You defined certain variables in particular ways. These choices inevitably shape your findings.
The question is whether you’re transparent about those trade-offs or whether you hide them.
Many researchers avoid discussing limitations because they fear undermining their work. If I acknowledge that my sample is not representative, won’t that weaken my contribution? If I admit I couldn’t access certain data, won’t that damage my credibility?
The opposite is true. When you hide limitations, editors assume you didn’t think about them. When you hide assumptions, editors assume your methodology is built on shaky ground. The researcher who explicitly acknowledges constraints while explaining why their work remains valid demonstrates integrity and sophisticated thinking.
Consider the difference:
“We analyzed 200 news articles from three major publications.”
Versus:
“We analyzed 200 news articles from three major publications selected for their national reach and coverage breadth. This approach allowed us to examine patterns in mainstream discourse but cannot represent niche or regional media. We acknowledge this limitation; our findings address how major institutional voices frame this issue, not how all media represent it. This is precisely what our research question asks.”
The second approach is longer, but it’s defensible. Editors can trust this researcher’s thinking because they can see it.
Pain Point 3: Reproducibility as Credibility
Here’s what editors are really checking: could another researcher follow your methodology and arrive at similar results?
If the answer is no, your work isn’t reproducible. And non-reproducible research is either sloppy or suspicious. It fails the basic test of scientific integrity.
Many researchers write methodology sections so vaguely that reproducibility is impossible. They describe their analytical approach in general terms without specifying actual processes. A qualitative researcher might write, “we analyzed data for themes” without explaining how themes were identified, defined, or verified. A quantitative researcher might mention statistical tests without specifying assumptions, parameters, or decision rules.
When your methodology is this vague, editors assume you’re hiding something. Maybe you didn’t actually follow a rigorous process. Maybe your results are sensitive to analytical choices you’re not disclosing. Maybe you can’t replicate your own work.
Transparency about the process builds trust. When you specify exactly what you did, how you did it, and why you did it that way, editors recognize you as someone who takes your work seriously.
Pain Point 4: The Unstated Positionality Problem
In qualitative research, especially, your position shapes your interpretation. Your background, your biases, and your theoretical commitments influence how you see data. Researchers often pretend this isn’t true, as if objectivity is possible if you just follow procedures.
But editors know better. They know that your positionality matters. And they know that ignoring it signals either naivety or dishonesty.
When you don’t discuss positionality, editors wonder: What is this researcher not seeing because of their background? What interpretations might be shaped by unstated assumptions? Have they considered alternative explanations for their findings?
Researchers who explicitly address positionality say something like: “As a researcher trained in institutional theory, I approached this data asking how organizations maintain legitimacy. Another researcher trained in critical theory might ask how organizations exploit power. Both interpretations are valid given the data. Here’s how my theoretical framework shaped what I noticed.” This transparency doesn’t weaken the work. It strengthens it by showing sophisticated methodological thinking.
Pain Point 5: Methodological Choices Without Justification
Here’s the pattern editors see repeatedly: a researcher makes a methodological choice, then fails to justify it against alternatives.
You chose purposive sampling instead of random sampling. You selected three case studies instead of five. You used thematic analysis instead of discourse analysis. You set your statistical significance threshold at p<0.05. Each choice shapes your results.
But you never explain why. You don’t address what you would have gained or lost by choosing differently. You don’t show that you considered alternatives and rejected them for reasons. You simply made a choice and moved forward.
This silence creates doubt. Did you choose this method because it was methodologically sound, or because it was convenient? Did you consider other approaches, or did you just pick the first one that came to mind? Do you understand why this method was appropriate for your research question?
When editors read an unjustified methodology, they read it as one of three things: careless work, methodological naivety, or deliberate opacity (perhaps you knew another method would give different results). None of those interpretations lead to acceptance.
Pain Point 6: Disconnection Between Research Question and Method
Your research question asks one thing. Your methodology does something else. These don’t align, but you never acknowledge the gap.
You’re asking “Why do organizations adopt this policy?” but your methodology collects individual interviews without examining organizational structures. You’re investigating causal mechanisms, but your method generates correlational data. You’re studying organizational change, but your study is cross-sectional.
Editors see these misalignments immediately. They wonder: does this researcher not understand their own research question? Do they not grasp what their chosen method can and cannot do? Are they trying to answer a question their methodology cannot address?
When your methodology connects clearly to your research question, showing editors exactly how your chosen approach will answer what you’re asking, they see careful thinking. When there’s a gap between the question and method, they see careless work.
What Methodological Soundness Actually Means
Methodological soundness is not about perfection. It’s about transparency, justification, and integrity.
It means explaining why you chose this method over alternatives. It means acknowledging limitations honestly without letting them undermine your work. It means showing that your methodology directly addresses your research question. It means demonstrating that you understand your own approach deeply enough to defend it against scrutiny.
Methodological soundness says: “I made deliberate choices for reasons I can articulate. I understand both the strengths and constraints of my approach. My work can withstand examination.”
Three Critical Changes to Your Methodology Section
1. Justify every choice. For each major methodological decision, explain why you made that choice and what you would sacrifice by choosing differently. Show editors that you thought this through.
2. Address limitations directly. Don’t hide constraints. Explain what they are and why your work remains valid despite them. This signals integrity and sophisticated thinking.
3. Connect to your research question. Make explicit how your methodology answers what you’re asking. Show editors that your chosen approach is the right tool for your specific research question.
Your methodology section is where editors evaluate whether you’re a careful researcher or someone going through motions. Write it as if you’re defending your choices to someone skeptical. Because you are. And that defense is what gets papers accepted.