What Happens After You Submit Your Paper to a Journal

You've spent months (maybe years) on your research. You've written the paper, revised it dozens of times, and finally hit that submit button.

Now what?

The waiting game begins. But it's not just empty waiting - there's a whole process happening behind the scenes. Here's exactly what happens to your manuscript from the moment you submit it until you see that final decision.

The moment you hit submit

You'll get an immediate confirmation email with a manuscript number. Something like "JBIOL-2024-12345" or "Nature-Med-2024-0987." Save this number - you'll need it for all future correspondence.

The journal's submission system will show your paper's status as "Submitted" or "Under Review." Don't expect much action for the first few days.

Your paper joins a queue. How long that queue is depends on the journal, the season, and honestly, luck. December submissions often sit longer because editors are on holiday. January and September can be busy as everyone returns from breaks.

The desk review (week 1-4)

Before your paper reaches any external reviewers, it goes through what's called a desk review or initial screening.

The handling editor (sometimes called the associate editor) does a quick assessment. They're asking three main questions:

Does this fit our journal's scope? If you submitted a computer science paper to a biology journal, it's getting rejected here. This sounds obvious, but you'd be surprised how often it happens.

Is the quality high enough for peer review? They're looking for basic things like proper methodology, clear writing, and sufficient novelty. If your methods section is two sentences long, that's a red flag.

Is this potentially interesting to our readers? Even if it's technically sound, if it's too niche or incremental, some journals will desk reject it.

About 30-50% of submissions get desk rejected at top-tier journals. Nature desk rejects about 70% of submissions, while PLOS ONE uses a rigor-only review process with much lower desk rejection rates. The editor will send you a brief email explaining why. These rejections usually happen within 1-4 weeks.

If you get a desk rejection, don't take it personally. Often it's just a mismatch between your paper and the journal. Check out our guide on common desk rejection reasons to understand what went wrong.

Reviewer assignment (week 2-6)

If your paper passes the desk review, the real work begins. The editor needs to find 2-4 external reviewers who can evaluate your work.

This is harder than it sounds.

The editor starts with a list of potential reviewers. They might use:

• Authors you cited in your references
• People who've published similar work recently
• Members of the journal's editorial board
• Recommendations from their network

But here's the catch: most people they ask will say no.

Reviewers are unpaid volunteers. They're busy with their own research, teaching, and life. The good reviewers - the ones you actually want reading your paper - are constantly being asked to review. They might already be handling 5-10 reviews this year.

The editor sends out invitations. "Would you be willing to review this manuscript on X topic? The deadline would be Y date."

Maybe 1 in 3 people will say yes. Sometimes it's worse.

This is why the reviewer assignment phase can take weeks. The editor isn't being slow - they're just struggling to find qualified people who'll actually do the work.

Pro tip: When you submit your paper, you can usually suggest reviewers. Do this. Suggest 4-6 people who know your field but aren't your direct collaborators. Make the editor's job easier.

The peer review period (month 2-6)

Once the editor finds reviewers, they send out your manuscript with a deadline. Usually 3-4 weeks for the initial review.

But reviewers are human. They get busy, travel, forget. Most journals expect about half their reviewers to miss the first deadline.

The editor sends reminder emails. Sometimes they have to find replacement reviewers if someone goes completely silent.

Here's what reviewers are actually doing during this time:

Reading your paper thoroughly. Good reviewers read it 2-3 times. Once for general understanding, once to take detailed notes, once to write their review.

Checking your methods. They're asking: Did you do this experiment correctly? Are the controls appropriate? Can I reproduce this from your description?

Evaluating your claims. Do your results actually support your conclusions? Are you overselling your findings?

Assessing significance. Is this work important enough for this journal? Does it advance the field meaningfully?

A thorough review can take 8-20 hours of work. Good reviewers take this seriously.

Meanwhile, you're checking the submission portal obsessively. The status might change from "Under Review" to "Reviews Being Processed" or something similar. This usually means reviews are coming in.

The editorial decision (month 3-6)

The editor collects all the reviews and makes a decision. The main options are:

Accept (rare). Your paper is basically perfect as-is. This happens to maybe 5-15% of submissions, and usually only for really strong work or perfectly executed studies.

Minor revision. The reviewers found some issues, but nothing major. You might need to clarify methods, add a control experiment, or fix some figures. Timeline: 2-4 weeks to revise.

Major revision. Significant concerns that require substantial additional work. Maybe you need new experiments, different statistical analyses, or major rewriting. Timeline: 2-6 months to revise.

Reject. Either the reviewers found fundamental flaws, or the work isn't suitable for the journal. Sometimes the editor will suggest alternative journals.

The decision email includes the reviewer comments. These can range from helpful and constructive to... less so.

Don't panic if the reviews seem harsh. Most papers get major revision on the first round. It's normal.

The revision process

If you get revisions, you now have real work to do.

Read all the comments carefully. Don't just skim. Print them out, highlight key points, make notes.

Address every single comment. Even if you disagree, you need to explain why. Reviewers notice when you ignore their feedback.

Write a detailed response letter. Go point-by-point through each reviewer's comments. Quote their original comment, then explain what you changed or why you didn't change it.

Be respectful but confident. You don't have to accept every suggestion, but you need to justify your decisions with data or logic.

Most revised papers get accepted, especially if you've addressed the concerns thoughtfully. But some go through multiple rounds of revision.

For detailed guidance on this process, check out our guides on responding to reviewer comments and major vs minor revision strategies.

Acceptance and production (1-3 months post-acceptance)

Your paper was accepted. But you're not done yet.

Copyediting. The journal's staff will edit your paper for grammar, style, and formatting. They might ask clarifying questions about unclear sentences.

Proofs. You'll get a PDF of how your paper will look in print. Check everything carefully - figure placement, author names, affiliations. This is your last chance to catch errors.

Publication. First online, then in print (if the journal still does print). Online publication usually happens 2-8 weeks after acceptance.

Some journals have "fast track" options for urgent or high-impact work - Lancet is known for particularly fast decisions on urgent medical research - but most follow this standard timeline.

What to do while you wait

Don't contact the editor every week. Most journals provide estimated timelines. Wait until you're 2-4 weeks past their estimate before inquiring.

Keep working. Don't put your research on hold while waiting for reviews. Start your next project.

Check the journal's status page. Many journals publish average review times or current delays.

Don't submit to another journal simultaneously. This is considered unethical in most fields.

Prepare for revisions. Think about potential experiments reviewers might request. Get ready.

What NOT to do

Don't argue with editors about desk rejections. They're rarely overturned, and you'll just waste time.

Don't blame reviewers for being slow. The editor is managing the timeline, not the reviewers.

Don't submit the same paper to multiple journals at once. Wait for a decision before trying elsewhere.

Don't take harsh reviews personally. Focus on the scientific content, not the tone.

The reality check

This process is frustrating. It's slow, unpredictable, and sometimes unfair. Good papers get rejected. Mediocre papers sometimes get accepted at top journals.

But it's also the best quality control system we have in science. Those reviewer comments, even the annoying ones, usually make your paper better.

Typical timeline from submission to publication: 6-18 months. Yes, really. Plan accordingly.

The wait times vary enormously between fields and journals. Check our review timelines database to see average times for specific journals.

Managing expectations

If this is your first submission, expect it to take longer than you think. First papers often need more revision rounds because you're still learning the unwritten rules of scientific writing.

Most papers don't get accepted on the first try. That's normal. Even experienced researchers face rejections regularly.

The key is persistence and learning from feedback. Each revision, each rejection, each reviewer comment teaches you something about how to communicate your science better.

How to avoid the long wait

Most of the time spent after submission is not in active review: it's waiting for editors to find reviewers who agree to participate, then waiting for those reviewers to write their reports. The median time to first decision is 30-90 days for most journals.

If your manuscript has issues that peer reviewers are likely to flag, you will wait three months and then restart the process with a major revision or rejection. Pre-submission review short-circuits that. A Manusights review takes 3-7 business days, replicates what a peer reviewer at your target journal would say, and gets you to a decision before you submit: not after.

See how pre-submission review works →

Related reading

• Desk Rejected? Here's Why - the most common reasons and how to avoid them
• How to Write a Cover Letter That Gets Your Paper Reviewed - first impressions matter
• Journal Acceptance Rates by Field - know what you're up against

Still waiting on reviews? Manusights pairs you with experienced reviewers who can pre-review your manuscript before you submit, catching problems that slow down or kill papers. Better to find issues on your terms than the journal's.

The Bottom Line

The post-submission process is largely out of your hands once you click send. What isn't out of your hands is the preparation before that. The submissions that move smoothly through editorial review are the ones where scope, framing, and methods quality were clearly in order from the first read.

Sources

• Published editorial guidelines from high-impact journals
• International Committee of Medical Journal Editors (ICMJE) reporting standards
• CONSORT, PRISMA, STROBE, and ARRIVE reporting guidelines
• Pre-Submission Checklist , 25-point audit before you submit

See also

• Peer Review Process Explained
• Major vs Minor Revision
• How to Respond to Reviewer Comments