Manuscript Submission Process: A Step-by-Step Guide

The manuscript submission process is the sequence of administrative and system-level steps an author works through between finishing a manuscript and getting it into a journal’s peer-review pipeline: assembling the required files, writing a cover letter, entering data into the journal’s online submission portal, and tracking the manuscript through initial editorial screening. It is distinct from a journal’s author guidelines, which specify WHAT a manuscript must contain (authorship criteria, disclosures, data statements, reference style). This guide covers the mechanics of HOW that finished manuscript actually gets from your desktop into a journal’s system and in front of an editor.

Before you start: what to have ready

Most submission systems will not let you save meaningful progress on an incomplete entry, and re-entering data after a timeout is a common source of frustration. Assembling the following before opening the portal makes the process considerably faster:

• The manuscript file(s) formatted to the journal’s specifications — many systems still require separate title page, blinded manuscript (for anonymized peer review), and figure files rather than one combined document. Figure-specific technical requirements (resolution, file format, colour mode) are covered in Scientific Figure Rules for Journal Submission.
• A complete author list with ORCID iDs. Most major submission systems (ScholarOne, Editorial Manager, OJS-based systems) now require or strongly encourage every author to sign in with or link an ORCID iD during submission — see ORCID Sign-In / Authentication and, if any co-author doesn’t yet have one, how to register an ORCID iD before you start.
• Author contribution statements. An increasing number of journals collect CRediT roles directly in the submission form rather than as free text in the manuscript.
• Corresponding author confirmed and reachable. The person who submits is not automatically the corresponding author of record in every system — check who the journal will treat as the point of contact; see Corresponding Author Responsibilities and the Corresponding Author definition.
• Disclosures — conflicts of interest, funding sources, and (where applicable) an AI-assistance disclosure statement, in the format the journal specifies.
• A cover letter (see below).
• Suggested and/or opposed reviewers, if the journal’s system asks for them, with institutional email addresses and a brief note on relevant expertise for each.
• Confirmation from every author that they have seen and approved the final version being submitted, and that the work is not under consideration elsewhere.

The cover letter

The cover letter accompanies the manuscript into the editor’s queue and is where authors typically state the manuscript’s significance, confirm it fits the journal’s scope, and make required declarations. Two declarations are close to universal: that the manuscript is not currently under consideration at another journal, and that all listed authors have approved submission — this maps directly to the ICMJE’s guidance on overlapping publications, which treats undisclosed simultaneous submission as grounds for prompt rejection or, if discovered after publication, retraction.

Beyond those universal elements, cover letter content is genuinely publisher-specific — a real point of variation worth knowing before you write one. Elsevier’s own author guidance states a cover letter “should not include funding information, author declarations, or suggested or opposed reviewers” — those belong in dedicated fields elsewhere in the submission system. Springer Nature’s guidance takes the opposite position: it explicitly names the cover letter as the place to “recommend or exclude reviewers (including the reasons why).” Check the specific journal’s instructions rather than assuming one convention applies everywhere. The full breakdown of required and optional cover letter elements is covered in Cover Letter for Journal Submission.

Working through the online submission system

Journals in most disciplines now route submissions through one of a small number of manuscript-tracking platforms — ScholarOne Manuscripts, Editorial Manager, or an OJS-based (Open Journal Systems) portal are the three an author is most likely to encounter, and the journal’s site dictates which one you use; authors don’t choose. The three differ in interface and terminology, but the underlying workflow an author steps through is broadly consistent:

1. Create or sign in to an account, usually via ORCID authentication or an email/password combination tied to the publisher.
2. Select the article type (original research, review, brief communication, case report, etc.) — this determines which downstream fields and word/figure limits apply, so get it right first.
3. Enter manuscript metadata: title, abstract, keywords, and classification/subject categories the journal uses for editor and reviewer assignment.
4. Enter the full author list, with affiliations, ORCID iDs, and the designated corresponding author.
5. Upload files in the order and format the system specifies — most systems auto-assemble a single PDF proof from your uploaded files for you to check before final submission; review it carefully, since formatting errors introduced at this step are a common cause of a manuscript being sent back for technical correction.
6. Enter or confirm disclosures — funding, conflicts of interest, ethics approval/consent statements, data availability statements, and AI-assistance disclosures where applicable.
7. Suggest or oppose reviewers, if the field is offered (see below).
8. Upload the cover letter as a separate file, where the system doesn’t provide a dedicated text field for it.
9. Complete required declarations/checkboxes and submit.

A detailed feature-by-feature comparison of ScholarOne, Editorial Manager, and OJS — useful if you’re evaluating platforms rather than simply submitting to a journal that has already chosen one — is in Editorial Manager vs ScholarOne vs OJS: Manuscript Submission Systems Compared.

Suggesting peer reviewers

Many submission systems ask authors to name potential reviewers, sometimes alongside reviewers to exclude (e.g. close collaborators, or individuals with a documented conflict). It’s worth understanding what this field is and isn’t for: under the ICMJE’s Recommendations on Responsibilities in the Submission and Peer-Review Process, the editor — not the author — is responsible for selecting appropriate reviewers, and a journal is under no obligation to use an author’s suggestions. Author-suggested reviewers are a convenience the editor may draw on, not a guarantee of who will review the work. When suggesting reviewers, list people with genuine subject-matter expertise and no conflict of interest with any author, and provide institutional (not personal) email addresses. See Peer Reviewer: Role, Responsibilities, and How to Become One and Peer Review: What It Is, How It Works, and Why It Matters for more on how reviewers are selected and what they’re expected to do.

What happens after you click submit

A submitted manuscript typically passes through an initial technical/editorial screening before it reaches peer review — checks for completeness, adherence to formatting requirements, plagiarism-detection screening, and basic scope fit. A manuscript can be returned to the author for technical correction at this stage without ever reaching a handling editor, or can be desk-rejected by an editor as out of scope or below the bar for full review, again without going to peer reviewers. If it clears initial screening, it’s assigned to a handling editor, who is then responsible — per the ICMJE — for selecting reviewers and ensuring they can access everything needed to evaluate the manuscript fairly, and for making the eventual editorial decision; ICMJE is explicit that a journal is not bound to follow reviewer recommendations either way. Throughout this stage, editors are expected to keep the manuscript’s existence and content confidential, sharing it only with authors and reviewers.

Common reasons a submission gets returned before review

• Missing or incomplete author disclosures (competing interests, funding, ethics approval)
• Figures or tables that don’t meet the journal’s technical specifications
• Reference list formatting that doesn’t match the journal’s required style
• Word count, structured-abstract, or article-type limits exceeded
• A cover letter or declaration missing a required statement (e.g. not confirming the work isn’t under consideration elsewhere)
• Author list or ORCID information incomplete or inconsistent across the manuscript and the submission form
• Manuscript scope doesn’t match the journal, evident on a first read

Most of these are avoidable by working from the journal’s own author guidelines as a checklist while assembling the submission, rather than treating it as background reading done once and forgotten.

Pre-submission checklist

• Manuscript formatted to the target journal’s structure and style requirements
• Title page, abstract, and keywords finalized
• All figures/tables meet the journal’s technical specifications
• Reference list and in-text citations match the journal’s required style
• Every author’s ORCID iD confirmed and affiliation current
• Corresponding author designated and contact details correct
• Conflict-of-interest, funding, ethics-approval, and data-availability statements drafted
• AI-assistance disclosure prepared, if any generative AI tool was used in preparing the manuscript
• Cover letter drafted, checked against this specific journal’s guidance on what it should and shouldn’t contain
• Suggested (and, if relevant, opposed) reviewers identified, with institutional emails
• All authors have reviewed and approved the final version being submitted
• Confirmed the manuscript is not under simultaneous consideration elsewhere

Frequently asked questions

Is the manuscript submission process the same as a journal’s author guidelines?

No. Author guidelines specify what the manuscript itself must contain and how it must be structured — authorship criteria, disclosures, data statements, formatting. The submission process is the separate administrative sequence of getting that already-compliant manuscript into the journal’s system: the cover letter, the online portal steps, reviewer suggestions, and what happens during initial editorial screening. See Author Guidelines: What Journals Require and How to Meet Them for the requirements side.

Can I choose which submission system a journal uses?

No — the journal has already selected a platform (commonly ScholarOne, Editorial Manager, or an OJS-based system), and every author submitting to that journal uses it. See Editorial Manager vs ScholarOne vs OJS for how the major platforms compare, which is more relevant if you’re advising a journal or editorial office than if you’re simply submitting a paper.

Do I have to suggest reviewers?

It depends on the journal — some make the field mandatory, others optional, and some don’t offer it at all. Where it’s offered, treat it as a genuine suggestion rather than a guarantee: per ICMJE guidance, reviewer selection is the editor’s responsibility, and a journal is not obligated to use author-suggested names.

What should a cover letter never include?

This varies by publisher rather than following one universal rule — Elsevier’s guidance explicitly excludes funding information, author declarations, and reviewer suggestions from the cover letter, while Springer Nature’s guidance explicitly includes reviewer recommendations. Always check the specific journal’s cover letter instructions rather than reusing a template across publishers. See Cover Letter for Journal Submission for a full breakdown.

Can I submit the same manuscript to more than one journal at once?

No. The ICMJE’s Recommendations on Overlapping Publications treat undisclosed concurrent submission as grounds for prompt rejection, or retraction if it’s discovered after publication. Wait for a decision (or a formal withdrawal) from one journal before submitting elsewhere.