The Journal Submission Process, Step by Step: From Cover Letter to Editorial Decision

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The Journal Submission Process, Step by Step: From Cover Letter to Editorial Decision

Publication of research manuscripts is a well-organized chain of decisions that starts even before the manuscript enters the journal submission process. This chain includes such actions as choosing a relevant journal, preparing the manuscript in accordance with the journal’s guidelines, completing ethical statements and disclosures, submitting a customized cover letter, and undergoing editorial screening and peer reviewing. Understanding the journal submission process is therefore important for researchers preparing their work for publication.

Moreover, the process is getting increasingly oriented towards research integrity, transparency, data availability, and responsible artificial intelligence (AI). The latest changes in the ICMJE Recommendations were made in January 2026, and they include new recommendations on AI in publishing and authors’ access to data. [1]

1. Select the Right Journal Before Submission

The choice of journal should consider first scientific and methodological suitability rather than only the impact factor and time to publication. [2]

The author should consider:

Scope and audience of the journal
Type of the article and manuscript restrictions
Publications in the field of research recently published
Publication and ethics policy
Open access and article processing charges
Peer-review process and publication policy
Indexing, editorial board, and credibility of the journal

Selecting the appropriate journal is one of the first and most important stages in the submission to publication guide, as it can influence the overall manuscript submission timeline and editorial decision process.

2. Prepare the Manuscript to Journal Standards

Once the journal has been chosen, the manuscript needs to be adjusted according to the current guidelines for authors.

While for an original study, the IMRAD structure still prevails as one of the popular scientific structures, yet there can be differences from article to article and from journal to journal. In addition, the Methods section should contain enough information about how the study was done and why. [3]

Pre-submission quality checks

Component	Key Requirement
Manuscript	Correct structure, word count and formatting
Abstract	Accurate summary aligned with the manuscript
References	Complete, current and correctly formatted
Tables/Figures	Correct numbering, captions and resolution
Ethics	Approval and consent information where applicable
Funding	Complete funding disclosure
Conflicts	Financial and non-financial relationships declared
Data	Appropriate data availability statement
Reporting	Relevant reporting checklist completed
AI use	Disclosure according to journal policy

Following these requirements is an essential part of understanding how to submit a manuscript to a journal and preparing it for the later peer review stages.

3. Prepare a Strong Cover Letter

The cover letter is the author’s communication to the editor, which needs to tell the editor why the manuscript deserves to be published in the journal.

The cover letter must contain:

Manuscript title and type of article
Research question and main findings
How it fits the journal
Originality and status of submission
Any ethical, financial, conflict of interest or other information that may help the editor decide about the manuscript

A clear cover letter for journal submissioncan help the editor quickly understand the relevance, originality, and important ethical or disclosure information associated with the manuscript.

4. Complete the Online Submission

Most journal submission portals use electronic systems which involve entering manuscript metadata along with uploading files.

Common manuscript submission criteria are:

Author names, affiliations and ORCID details
Details of corresponding authors
Abstract and keywords
Manuscript and supplementary files
Funding details
Declaration of conflict of interest
Ethical approvals and consent statement
Data availability statement
Reporting guidelines
Cover letter

It is advisable for authors to review the automatically created PDF manuscript file or submission preview before making the final submission to verify that figures, tables, supplementary files, and author metadata are correct.

5. Editorial Screening: The First Decision Point

The act of submission does not imply automatic peer review. The editors may first carry out an initial assessment that includes:

Relevance of the journal
Quality and novelty of the science
Completeness of the manuscript
Ethical considerations
Specific reporting requirements
Concerns about research integrity
Plagiarism markers
Data and disclosure requirements

Thus, the submission may be rejected by the editorial board even before peer review because of the irrelevance to the journal, lack of meeting certain requirements, and non-provision of novel science. These steps form an important part of how to submit a manuscript to a journal, particularly because errors in the online submission can delay the manuscript submission timeline.

6. Current Trend: AI Disclosure and Author Accountability

The growing presence of artificial intelligence (AI) in scientific publishing makes disclosure and responsibility of the author integral parts of the process of preparing and submitting the manuscript. The process of disclosing the use of AI must not be viewed as a distinct chronological step in journal submission. Instead, the disclosure of the use of technologies assisted by AI should be done in the cover letter and in the corresponding part of the manuscript in compliance with the journal’s guidelines. In case any AI technologies are applied in carrying out, analysing, or other processes that pertain to research, the same should be disclosed in the Methodology section or any other relevant sections.

According to ICMJE recommendations of 2026 [1], authors must disclose AI-assisted technologies applied for the creation of submitted articles and explain their application in the cover letter and corresponding part of the manuscript. AI technologies cannot be listed as authors since AI cannot take responsibility for accuracy, integrity, and originality.

Therefore, researchers should:

check the AI policy of the target journal prior to submission;
disclose AI assistance if necessary;
confirm information generated by AI.
have human responsibility for the manuscript.

If the research uses AI to gather data, analyse results, or create figures, this should be disclosed in the Methods section.

7. Peer Review and Reviewer Assessment

If the manuscript passes editorial screening, it may be sent to independent reviewers. Reviewers commonly assess the research question, methodology, statistical analysis, interpretation, originality, reporting quality and significance. [5]

Evaluation Area	Typical Question
Research question	Is the question clear and relevant?
Methodology	Is the design scientifically appropriate?
Data analysis	Are analytical methods justified?
Results	Are findings presented accurately?
Discussion	Are conclusions supported by evidence?
Originality	Does the study contribute something meaningful?
Reporting	Is sufficient methodological detail provided?

Peer review also involves strict confidentiality. ICMJE guidance states that reviewers should not publicly discuss submitted manuscripts or upload confidential manuscripts to AI systems where confidentiality cannot be assured unless the journal permits such use. These activities represent the main peer review stages through which a manuscript may pass before an editorial decision is reached.

8. Understanding the Editorial Decision

After editorial assessment and peer review, the editor communicates a decision.

Decision	Meaning	Author Response
Accept	Manuscript is accepted	Complete production requirements
Minor Revision	Limited changes required	Address comments carefully
Major Revision	Substantial changes required	Revise manuscript and response letter
Reject & resubmit	Significant redevelopment required	Rework before potential resubmission
Reject	Manuscript is not accepted	Revise and consider another suitable journal

A revision decision should not be viewed simply as criticism. It provides an opportunity to strengthen methodological clarity, reporting quality and scientific interpretation. Understanding the editorial decision process helps authors prepare appropriately for acceptance, revision, rejection and resubmission.

9. Responding to Reviewer Comments

A good revision would also have an organised response to the reviewer’s comments.

The response to a reviewer’s comment should include:

Reviewer’s comment → Response → Modification → Location in the manuscript

In case of disagreement with a reviewer’s comment, the response must be professional and scientific backed. It is important not to make any unnecessary modifications. A structured response can help move the manuscript efficiently through the peer review stages and may influence the subsequent editorial decision. [6]

10. Emerging Trends in Journal Publishing

Increased attention is paid in digital research and publishing to such aspects as transparency, reproducibility, responsible AI application, and data accountability in research. These tendencies include:

Higher degree of disclosure regarding the application of AI and accountability of authors.
Improved availability and accountability of data.
Growing importance of transparent approaches and reproducibility.
More frequent application of automated research integrity checking and reporting requirements.
Increased confidentiality and integrity of peer reviews.
Such tendencies can be considered part of the changing standards of publication required for research integrity.

Connect with us to explore how we can support you in maintaining academic integrity and enhancing the visibility of your research across the world!

Conclusion

The submission process to a journal is an extensive process that includes many steps from selecting a journal to making an editorial decision, rather than just uploading the paper. Scientific merit is a prerequisite, but successful publication requires not only scientific merit but also transparency of methods, ethics, accuracy, responsible authorship, data accountability, and communication with editors and reviewers.

In today’s world of scientific publication, there are additional factors related to expectations regarding AI technologies, data availability, and research integrity that the author should be aware of and prepare for before submission.

Pubrica supports researchers with journal selection, manuscript preparation, AI disclosure, data transparency, and submission requirements to help ensure a smooth and compliant publication process. Get expert publication support from Pubrica today.

Frequently Asked Questions (FAQs)

1. What is the journal submission process?

The journal submission process involves selecting a suitable journal, preparing the manuscript according to its guidelines, completing ethical and disclosure requirements, writing a cover letter, submitting the manuscript through the journal’s online system, and going through editorial screening and peer review.

2. How do you submit a manuscript to a journal?

To understand how to submit a manuscript to a journal, first choose an appropriate journal and follow its author guidelines. Prepare the manuscript, abstract, references, figures, tables, ethical statements, funding and conflict-of-interest disclosures, data availability statement, and cover letter. Then upload the required files through the journal’s submission system and carefully check the submission preview before finalizing it.

3. What should be included in a cover letter for journal submission?

A cover letter for journal submission should generally include the manuscript title and article type, research question, key findings, relevance to the journal, originality, and confirmation regarding the submission status. It should also disclose relevant ethical, financial, authorship, or conflict-of-interest information where required.

4. How long does the manuscript submission timeline take?

The manuscript submission timeline varies between journals and depends on factors such as editorial screening, reviewer availability, revisions, and the journal’s publication workflow. Some manuscripts may receive an initial decision quickly, while the complete process from submission to publication can take several months or longer.

5. What are the main peer review stages and editorial decisions?

The main peer review stages usually begin after the manuscript passes initial editorial screening. Reviewers evaluate the research question, methodology, data analysis, results, originality, and reporting quality. The editorial decision process may result in acceptance, minor revision, major revision, reject and resubmit, or rejection. Authors should respond carefully and professionally to reviewer comments when revisions are requested.

References

(N.d.). Icmje.org. Retrieved September 4, 2026, from https://www.icmje.org/
Ramia J. M. (2023). How to select a journal for your research. World journal of gastroenterology, 29(21), 3379–3384. https://doi.org/10.3748/wjg.v29.i21.3379
Macdonald, N. E., Ford-Jones, L., Friedman, J. N., & Hall, J. (2006). Preparing a manuscript for publication: A user-friendly guide. Paediatrics & child health, 11(6), 339–342. https://doi.org/10.1093/pch/11.6.339
BaHammam A. S. (2025). The Transparency Paradox: Why Researchers Avoid Disclosing AI Assistance in Scientific Writing. Nature and science of sleep, 17, 2569–2574. https://doi.org/10.2147/NSS.S568375
Zimba, O., & Gasparyan, A. Y. (2021). Peer review guidance: a primer for researchers. Reumatologia, 59(1), 3–8. https://doi.org/10.5114/reum.2021.102
Hidouri, S., Kamoun, H., Salah, S., Jellad, A., & Ben Saad, H. (2024). Key Guidelines for Responding to Reviewers. F1000Research, 13, 921. https://doi.org/10.12688/f1000research