How to Handle Conflicting Reviewer Comments: A Guide for Authors

How to Handle Conflicting Reviewer Comments in Peer Review

Introduction

Receiving your first decision letter from a journal can be both exciting and nerve-wracking. When you open it and find that one reviewer is enthusiastic while another is sharply critical, the experience can quickly become confusing and discouraging. Conflicting reviewer comments are common in peer review, particularly for interdisciplinary work, innovative methods, or contentious topics. Yet the way you respond to those comments can have a significant impact on whether your manuscript is ultimately accepted.

Rather than seeing conflicting feedback as a sign that your work has failed, it is often more helpful to view it as an indication that your paper engages different readers in different ways. Each reviewer brings their own expertise, assumptions, and preferences; their disagreements can reveal where your arguments need clarification, where your methods need stronger justification, or where your writing needs to guide readers more clearly.

This article offers a structured approach to handling conflicting reviewer comments. It explains why discrepancies arise, how to analyse them systematically, and how to craft a clear, respectful response that reassures editors that you have treated the feedback seriously and intelligently. It also includes example wording, a response-table template, and final checks before resubmission. Used thoughtfully, these strategies can help you transform conflicting comments into a roadmap for improving your manuscript.

Why Reviewer Comments Conflict

Peer reviewers are asked to evaluate the same manuscript but may approach it with different lenses. Some focus mainly on methodology, others on theoretical framing, statistical analysis, or practical implications. These differences can easily produce conflicting recommendations.

Common Types of Conflicting Reviewer Comments

1. Methodological discrepancies – One reviewer argues that your sample size is too small or your method inappropriate, while another states that the design is appropriate and robust.
2. Differences in interpretation – Reviewers draw different conclusions from the same data or disagree about how results should be framed and discussed.
3. Requests for additional work – One reviewer calls for extensive new experiments or analyses, while another considers your current dataset sufficient.
4. Writing and structure preferences – One wants a shorter, more focused discussion; another requests more detail or additional sections.
5. Opposing publication recommendations – One reviewer recommends acceptance (perhaps with minor revisions), while another recommends rejection.

Understanding which category your conflicting comments fall into is the first step toward developing a rational revision strategy.

Step 1: Read Everything Carefully and Calmly

When decision letters arrive, it is natural to feel defensive or disappointed—particularly if you invested substantial time and energy in the manuscript. Before you begin planning revisions, give yourself enough time to process this reaction. Then, re-read the editor’s letter and each reviewer report slowly and carefully.

As you read, highlight or annotate:

• comments that appear in more than one review (these are often high priority),
• points where reviewers directly contradict one another,
• issues that relate to core validity (methods, data, analysis) vs. presentation (clarity, structure, style).

At this stage, resist the temptation to argue mentally with the reviewers. Your goal is to understand their perspectives and map the landscape of the feedback.

Step 2: Discuss Feedback with Co-Authors and Mentors

If you are working with co-authors, share the decision letter and reviews with them. Schedule a meeting or online discussion dedicated specifically to planning your response. Each author may notice different strengths and weaknesses in the comments.

Questions to guide the discussion:

• Which points do we agree are valid and helpful?
• Where do we feel a reviewer may have misunderstood or overlooked something?
• Which conflicting comments are merely stylistic, and which relate to substantive scientific issues?
• Is additional analysis or clarification realistically possible within our time and resource constraints?

If you are a solo author or early-career researcher, consider seeking advice from a mentor or experienced colleague—especially for tricky methodological criticisms or conflicting recommendations. An independent reader can help you distinguish between strong and weak points in the reviews.

Step 3: Prioritise Comments by Importance, Not Volume

Not every comment carries equal weight. A short remark about a missing reference is less critical than a brief but substantive concern about bias in your sampling strategy. Similarly, a single serious methodological critique may matter more than several minor stylistic suggestions.

When prioritising:

• Give highest priority to issues that affect the validity, reliability, or ethical integrity of your study.
• Next, focus on comments that clearly align with the journal’s aims and guidelines (for example, reporting standards, required sections, or data availability).
• Then address comments that will improve clarity, readability, and structure, even if they are “only” about writing style.
• Finally, consider optional or subjective suggestions, especially when they conflict with each other or with the core logic of the paper.

Remember that the editor’s decision letter often indicates how they interpret the reviews and may hint at which points they consider most important. Re-read that letter carefully.

Step 4: Respond to Every Comment (Even When You Disagree)

Editors expect authors to respond to all reviewer comments, not just the ones they agree with. Failing to mention a point can be interpreted as ignoring it. Even when you decide not to implement a suggestion, you should acknowledge it and explain your reasoning.

A respectful, evidence-based response might look like this:

“We thank the reviewer for this thoughtful suggestion. We considered applying the alternative statistical method they proposed. However, based on our study design and guidance from [relevant source], we concluded that our original approach (described in Section 2.4) remains the most appropriate. To clarify this choice, we have expanded the explanation in the Methods section (Page 9, Lines 12–23).”

This type of response shows that you have taken the comment seriously, sought justification, and improved the manuscript accordingly, even if you did not make the exact change requested.

Step 5: Finding Common Ground Between Conflicting Comments

When reviewers disagree, your task is to look for underlying issues that can be addressed in a way that respects both perspectives. For example:

• If one reviewer wants more statistics and another is satisfied, you might keep your core analysis but add clearer justification of your chosen methods, perhaps with a short robustness check rather than a full re-analysis.
• If one reviewer finds your discussion too long and another wants deeper theoretical integration, you could streamline repetitive content while sharpening and expanding key conceptual points.
• If one asks for a new experiment and another calls your current dataset sufficient, you might explain more explicitly why additional data are beyond the scope of the present study, and outline planned future work instead.

In your response letter, you can explicitly acknowledge the conflict and explain your balanced solution:

“We note that Reviewer 1 requested additional experiments, while Reviewer 2 considered the existing dataset sufficient. Given the logistical and ethical constraints of collecting new data at this stage, we have instead expanded our discussion of limitations and future research (Page 18, Lines 4–19) and clarified the robustness of the present findings.”

Step 6: When to Seek Guidance from the Editor

Sometimes, reviewer comments are so strongly opposed that compromise is difficult, or you may be unsure which suggestion should be prioritised. In such cases, it can be appropriate to ask the editor for guidance.

When contacting the editor:

• Be brief and focused; editors are busy.
• Summarise the specific conflict objectively.
• Explain your tentative plan for addressing the comments.
• Ask politely whether this approach is acceptable or whether the editor would prefer a different solution.

For example:

“Reviewer 1 recommends re-analysing the data using Method A, while Reviewer 2 strongly prefers Method B. Our current analysis uses Method B, and we believe it is most appropriate for the reasons outlined below. We propose to retain Method B but add a clearer justification and sensitivity check. We would be grateful for your guidance on whether this approach aligns with the journal’s expectations.”

Editors appreciate authors who engage constructively and transparently with the review process.

Step 7: Maintain a Professional and Constructive Tone

The tone of your response letter matters. Reviewers volunteer their time, and editors must decide whether they want to continue working with you as an author. Professional, grateful, and measured language fosters goodwill—even in the face of criticism.

Helpful phrases (“Dos”):

• “We thank the reviewer for this insightful comment…”
• “We agree that this is an important point and have now…”
• “We acknowledge the concern raised and have addressed it by…”
• “We respectfully disagree with this point because…” (followed by evidence and clear reasoning)

Phrases to avoid (“Don’ts”):

• “The reviewer clearly misunderstood our research…”
• “We disagree and therefore ignored this comment.”
• “This request is unreasonable.”

Even when you feel a comment is unfair, framing your response diplomatically will help your case far more than emotional language ever could.

Step 8: Document Revisions Clearly and Transparently

A well-organised revision package makes life much easier for editors and reviewers and increases the likelihood of a positive outcome. Two tools are especially useful:

• Tracked changes in your word processor to highlight all modifications in the manuscript.
• A detailed response document (often a separate file) that lists each reviewer comment and your response, including where in the manuscript changes were made.

Example Response Table for Conflicting Comments

A table format is not mandatory, but it can help structure your response clearly. Whether you use a table or bullet points, always quote the reviewer comment (in full or in summary), then follow with your reply and a reference to where changes appear in the manuscript.

Step 9: Final Checks Before Resubmission

Before uploading your revised manuscript and response letter, complete a final quality check:

1. Re-read the editor’s letter and ensure that all major issues highlighted there have been addressed explicitly.
2. Verify that every reviewer comment appears in your response document and that no point—however minor—has been ignored.
3. Check consistency between your responses and the revised manuscript. If you say you have made a change, make sure it is clearly visible in the text.
4. Review language and clarity in both the manuscript and the response letter. This is an ideal stage to involve a human proofreading and editing service, especially if you are writing in a second language or responding to extensive comments.
5. Confirm formatting and submission requirements in the journal’s guidelines, including file types, naming conventions, and any deadlines for resubmission.

A thorough, well-presented revision demonstrates professionalism and increases the likelihood that reviewers will see your changes in a positive light.

Conclusion

Conflicting reviewer comments are an inevitable part of peer review, not a sign that your research has no value. When handled calmly and systematically, they can help you refine your arguments, clarify your methods, and strengthen the overall quality of your manuscript. The key is to analyse feedback carefully, seek advice from co-authors and mentors, prioritise substantive issues, respond respectfully to every comment, and, when necessary, involve the editor in resolving major conflicts.

By documenting revisions transparently and maintaining a constructive tone throughout your response, you show editors that you are a thoughtful, reliable contributor to the scholarly community. Combined with clear writing, rigorous methods, and expert human proofreading and editing, a well-managed response to conflicting reviewer comments can turn a challenging decision letter into an important step on the path to publication.