Nobody tells you this during your PhD. You survive the literature review, wrestle through the methodology, and finally get your results to make sense. And then, right when you think the hard part is over, someone hands you the Author Guidelines PDF for your target journal.
It’s 47 pages long.
Welcome to manuscript preparation for journal submission — the phase where good research goes to die if you’re not careful.
I’m half joking. But only half. A Wiley report from 2022 revealed that approximately 21% of submissions are rejected without reaching peer review. Not the science was bad. Because the formatting was wrong or the cover letter was too vague, or the authors didn’t follow one or more of the steps that the journal explicitly requests. One in five papers. Vanished before an abstract in a single reviewer’s eyes.
Pick the Right Journal First — Then Format
A lot of researchers do it backwards. They write their paper and format it according to their own preferences, and then try to find a journal that will accept it. That approach costs weeks.
Each journal has its own personality. Nature wants brevity and broad impact. PLOS ONE cares more about methodological soundness than wow-factor. A specialist journal in environmental chemistry probably doesn’t want your paper on urban sociology, no matter how good it is.
Elsevier’s Journal Finder and Springer’s Journal Suggester both let you paste your abstract and get a list of relevant publications. Takes five minutes. Saves you from a very demoralising desk rejection six weeks later.
Once you’ve locked in your journal, download their Author Guidelines. Not skim them. Actually read them. The section on reference formatting alone will tell you more about a journal’s standards than any impact factor ranking.
The Formatting Guidelines Are Not Suggestions
Every journal publishes its formatting guidelines for research papers, and they mean every word of it. Font size, line spacing, margin width, figure resolution, reference style — it all gets checked, usually before a human even looks at your work.
This is what appears to be common in those guidelines:
- Font: Times New Roman or Arial – usually 12pt.
- Spacing: double for most journals.
- Reference format: Is it APA, Vancouver, Harvard or something uniquely defined by the journal?
- Resolution of figures: min. 300 DPI (dots per inch) for print; 72 DPI for web-only is not acceptable in almost… any journal.
- Abstracts generally have a strict limit of 250 to 300 words.
- Supplementary files: yes, they have rules too
The citation style problem confuses more people than you’d expect. Zotero, Mendeley, and EndNote will also do this automatically after you have chosen your journal’s style.If in 2024 you’re still manually formatting references, for God’s sake stop. It’s just asking for errors.
One thing worth knowing: a formatting mistake doesn’t mean your paper is rejected on the spot. Some editors send it back for corrections. Others just… move on to the next submission. You don’t always get a second chance.
Get the Structure Right — IMRaD and Why It Works
Most empirical research articles are organised according to a so-called IMRaD structure (introduction, methods, results, and discussion). It is there because it is effective. Readers know where to find what they need. Reviewers can assess your methods without searching the entire paper.
Introduction
Start from the problem, not the history of the universe. Say what gap in knowledge you are addressing, why it is important now, and what you have done specifically. Conclude with a clear research question or hypothesis. Keep it tight.
Methods
Describe the procedures so that another scientist could repeat the study only by reading this part. No hand waving allowed. If relevant, indicate the software version used. If there were inclusion criteria for your sample, please enumerate them. Reviewers are tougher on this section than any other.
Results
Only the numbers please. And don’t resist the temptation to interpret. Strive for clarity in your results; use tables and figures to present your results where they truly help to clarify; and allow your results to speak for themselves — avoid editorialising.
Discussion
This is the place to tell readers what your findings mean, how they compare with the literature, and what the limitations of your study are. That last part contributes. Papers that admit limitations frankly are generally better received than papers that pretend all went perfectly. Reviewers are not fooled, and neither are the editors.
If putting this structure together is something you’d like professional support on, our research paper publication services are built exactly for this stage of the process.
Run a Plagiarism Check — Even on Your Own Previous Work
This step surprises early-career researchers more than anything else on this list. You’d think your own work is safe from plagiarism. It isn’t, technically.
Self-plagiarism — reusing paragraphs or sentences from your earlier published papers without citation — is a real concern in academic publishing. Journals use tools like iThenticate to catch it, and they flag it the same way they’d flag copying from another author. There are no unlimited rights associated with having created content, that is why the right to reuse it in a new submission always requires disclosure and it is considered self-plagiarism otherwise. it is the norm to run a plagiarism check prior to submission. Many large publishers (e.g., Elsevier, Springer) also do run their own plagiarism checks on manuscripts, so really you are just getting ahead of what they will find. Target a similarity score of less than 15 to 20 percent, although a few journals have stricter limits, so see the journal-specific policy. It won’t give you a similarity score, but it catches language issues that can make reviewers stumble — and anything that makes a reviewer stumble is a problem you don’t need.
The Cover Letter Is Your First Impression — Don’t Waste It
A shockingly large number of researchers treat the cover letter like a formality. One paragraph saying “please find attached our manuscript” and their name at the bottom. That is not a cover letter. That opportunity was lost.
A journal submission cover letter generally informs the editor of three things that they really want to know: what your manuscript is about, why it should be published in their journal in particular, and what makes your results significant enough to make its readers’ time worth spending on it.
This is what good cover letter should look like:
- Manuscript title (and article type if required: e.g. original research, systematic review, case report etc.)
- A two to three sentence summary of the main findings of the study — not the background, the results
- A made plain statement of relevance of the paper to the scope and audience of the journal
- Statement that the manuscript is not under review with any other journal
- Declarations of interests, sources of funding, and ethical approvals
- Suggested reviewers, if the journal accepts them (many do, and editors frequently make use of these suggestions)
Keep it short, one page. They receive several dozen of these a week. Well-crafted succinct cover letter will be more noticeable than an overly verbose one.
How to Actually Prepare for Peer Review
Peer review is a dirty word. Sloooooow, a bit harsh, occasionally mind-boggling. But reviewers are looking for certain things, and being aware of what they are looking for is really helpful preparation. Read five to ten recent papers from your target journal before submitting. See how they organize the Discussion. How do they handle conflicting evidence? How long are their Methods sections? What do their abstracts sound like? Your paper will be evaluated in the context of those papers. Make sure it belongs there.
Tips for preparing for peer review that I heard from some veteran researchers:
- Get someone who is not in your research group to read your Introduction and abstract. If they can’t follow it, they won’t a reviewer from a related field.
- You need a citation or your own data for every claim in your paper. Check them all.
- Figures and legends should be interpretable by themselves: “Without reading the text, the reader should be able to understand what the figures show”. A person flipping through figures and captions from your paper should be able to know what you have found, so make sure she can.
- When writing your finished paper, you should have it professionally edited if English is not your native language. Language is not a reason for rejection in most journals, but it is a reason to take longer to review and cause more frustration.
- Consider what the three strongest critiques of your methodology a potential reviewer could have — and rebut them in your Discussion before they do.
That last one is the most underused strategy in academic writing. You know your study’s limitations better than any reviewer does. Get ahead of them.
Go Through a Pre-Submission Checklist Before You Hit Submit
You’ve done the research. You’ve written the paper. You’ve run the plagiarism check and drafted a proper cover letter. Now, before you submit, slow down for ten minutes and go through a structured checklist.
This is where small, fixable things get caught. Missing ORCID IDs. A figure submitted at the wrong resolution. A file had been included but was not labeled. Declaration of ethics approval that should have been included, but wasn’t.
A full pre-submission checklist usually includes:
- Manuscript formatted to the journal’s exact specifications
- All author details complete, including ORCID IDs where required
- Abstract within the word count limit
- All figures at the required resolution and in the correct file format
- Supplementary materials properly labelled and referenced in the main text
- Ethical approval number included where relevant
- Plagiarism check completed and similarity score within acceptable range
- Brief cover letter completed, proofread and addressed to the appropriate editor.
- The final version has been seen and approved by all co-authors
For a ready-to-use, detailed checklist built specifically for academic journal submissions, see our Pre-Submission Checklist — it’s free and it covers everything above.
Mistakes That Get Papers Rejected Before Anyone Reads the Science
These come up so often it’s almost predictable at this point.
- Submitting to a journal that doesn’t cover your field — happens more often than it should
- Ignoring the word count and assuming editors won’t notice
- Using inconsistent terminology throughout the paper — calling the same concept three different things confuses reviewers
- Missing declarations: conflicts of interest, author contributions, and funding sources are not optional
- Figures submitted as low-resolution JPEGs
- Wrong reference format — even if every citation is accurate, the wrong style gets flagged
- A cover letter that was clearly written in two minutes
None of these require additional research to fix. They just require attention and a bit of time before submission. Most rejected papers that fall into this category could have avoided rejection entirely.
What Journal Editors Actually Notice
Editors read a lot of submissions. After a time, they acquire a very rapid sense of whether a manuscript has been written in a hurry or with care.
Some research paper publishing tips that are repeatedly heard when editors talk about what makes a submission stand out:
Write for the reader, not to yourself. You’re not trying to show off how much you know in a journal paper. It’s to communicate a finding clearly enough that someone else can build on it. Long sentences with six subordinate clauses are not a sign of intelligence. They’re a sign that the paper needs editing.
Don’t hide from your limitations. A paper that lists genuine limitations and explains how they were managed looks more rigorous than one that pretends none exist. Reviewers and editors have seen enough research to know when something has been glossed over.
Don’t rush. A paper submitted two weeks before it’s truly ready will almost always come back for major revisions. Two extra weeks of careful preparation can save you three months of revision cycles and a second round of reviews.
And if you don’t hear back within the journal’s stated review timeline, it’s fine to send a polite follow-up email to the editorial office. Professional, brief, no demands. Most editors respond well to that.
The Preparation Is Part of the Research
Manuscript preparation for journal submission isn’t separate from your research. It’s the final stage of it. Each part of this guide—the formatting, the plagiarism checks, the cover letter, the pre-submission checklist—is presenting your work in a way that allows it to be given a fair reading.
The science by itself isn’t sufficient.
The science alone isn’t enough. Plenty of solid studies don’t get published because the submission wasn’t handled well. And plenty of less groundbreaking papers do get published because the authors understood what journals need and delivered it cleanly.
You’ve put in the work. Now put in the preparation.
Submit with confidence — because you’ve actually checked everything.