Exporting Notes from Mendeley to Notion

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-27

Quick Answer

• Export Mendeley notes and annotations as a BibTeX file for references and a CSV file for note text, then import both into Notion using a structured database template.
• Use a custom Notion template with linked database relations to preserve the connection between each note and its source reference.
• PDF annotations and highlights do not transfer as visual markup, only the note text and metadata survive the migration.

Understanding the Mendeley to Notion Migration Problem

Researchers and students who maintain literature notes in Mendeley face a specific challenge when they want to consolidate their knowledge management into Notion. Mendeley stores two distinct types of information: bibliographic metadata about references and the notes you attach to those references. The desktop application also stores PDF annotations and highlights, but these exist as visual markup on the PDF file itself instead of as portable text data.

The migration problem has three layers. First, you need to extract the bibliographic data in a format that Notion can interpret. Second, you need to extract the note text in a way that preserves which note belongs to which reference. Third, you need to design a Notion structure that maintains those relationships after import.

Mendeley provides two export pathways that address the first two layers. The BibTeX export format captures citation metadata including authors, titles, journals, years, and DOIs. The CSV export format captures the notes you have written, along with the reference identifier that links each note to its source. Neither pathway preserves the visual PDF annotations themselves.

Understanding this limitation matters before you begin. If your workflow depends on seeing highlighted passages within the PDF context, you will need to keep Mendeley or another PDF reader as part of your system. If your workflow depends on the text of your notes and the ability to search and connect them, Notion can serve as a functional replacement.

At a Glance

Core Principles for Literature Note Migration

The migration from Mendeley to Notion follows the same logic as any data transfer between research tools. You are moving structured information from one system to another, and the quality of the destination structure determines how useful the data becomes.

The first principle is separation of data types. Bibliographic metadata and note text are different kinds of information. They need different handling during export and different database structures after import. Mixing them into a single flat file creates a system that is difficult to search and maintain.

The second principle is relationship preservation. A note without its source reference loses context. A reference without its notes loses the intellectual work you have done. The migration must preserve the link between these two data types, which means your Notion structure needs a relation property that connects the notes database to the references database.

The third principle is metadata completeness. The BibTeX export contains fields that you may not use immediately, such as abstract, keywords, and file paths. Keeping these fields in your Notion database gives you future flexibility for searching and filtering. Trimming the data during import is easier than recovering it later from the original export file.

The fourth principle is verification after migration. You should compare record counts between the source and destination systems. The number of references in Mendeley should match the number of records in your Notion references database. The number of notes should match as well. Discrepancies indicate that some records failed to import or that the CSV parsing missed rows.

Preparing Your Mendeley Library for Export

Before you export anything, review your Mendeley library for data quality issues that will carry into Notion. Duplicate references, incomplete metadata, and orphaned notes all create problems that are easier to fix before migration than after.

Check for duplicate references first. Mendeley sometimes creates multiple records for the same paper when you add it through different methods. Each duplicate will appear as a separate record in Notion, which fragments your note collection. Merge duplicates in Mendeley before exporting.

Check for missing metadata fields. References that lack DOIs, journal names, or publication years will still import, but they will be harder to search and sort in Notion. The BibTeX export includes empty fields for missing data, and those empty fields become empty properties in your Notion database.

Check for notes attached to references that you may want to exclude. If you have notes on references that are no longer relevant to your work, decide whether to delete them before export or filter them after import. Deleting before export reduces the amount of data you need to verify after migration.

Organize your library folders if you want to preserve some organizational structure. The BibTeX export does not include folder information, so any folder-based organization in Mendeley will not transfer. You can add a category or tag property to your Notion database after import to recreate this structure manually.

Exporting References as BibTeX

The BibTeX export from Mendeley creates a text file with citation entries for every reference in your selected scope. You can export your entire library or a specific folder or collection.

Open Mendeley Desktop and select the references you want to export. Use the File menu and choose Export. In the export dialog, select BibTeX as the format. Choose a file name and location that you will remember, then complete the export.

The resulting file contains entries that begin with an at sign followed by the entry type, such as article, book, or inproceedings. Each entry has a citation key and a series of fields in the format field name equals value. The fields include author, title, journal, year, volume, number, pages, doi, and abstract when those values exist in your Mendeley record.

The BibTeX file is plain text, which means you can open it in any text editor to inspect the contents before importing. This inspection step is useful for verifying that the export contains the expected number of entries and that the fields look complete.

Exporting Notes as CSV

The CSV export from Mendeley captures your notes in a tabular format. Each row represents one note, and the columns include the note text, the date the note was created or modified, and an identifier that links the note to its source reference.

Open Mendeley Desktop and select the references that have notes you want to export. Use the File menu and choose Export. In the export dialog, select CSV as the format. Choose a file name and location, then complete the export.

The CSV file can be opened in a spreadsheet application to inspect the contents. You should verify that the number of rows matches the number of notes you expect to migrate. You should also verify that the reference identifier column contains values that will match the citation keys in your BibTeX file.

One limitation of the CSV export is that it does not include the full bibliographic details of the reference. The note rows reference the source by an identifier, but the citation details live in the BibTeX file. This is why you need both exports to complete the migration.

Designing the Notion Database Structure

The Notion structure for your migrated literature notes should use two databases connected by a relation property. This design mirrors the relationship between references and notes in Mendeley while taking advantage of Notion's database features.

The first database stores references. Each record contains the bibliographic metadata from the BibTeX export. The properties include title, authors, journal, year, DOI, and abstract. You can add additional properties for tags, reading status, and personal ratings.

The second database stores notes. Each record contains the note text and a relation to the reference database. The relation property is what preserves the connection between a note and its source. You can add properties for note type, creation date, and topic tags.

The relation property in Notion can be configured as one-to-many, which means one reference can have many notes. This matches the Mendeley model where you can attach multiple notes to a single reference.

You also need a way to import the data into these databases. Notion does not have a native BibTeX importer, so you will use a conversion step. Several approaches exist, including using a spreadsheet application to convert the BibTeX data into a CSV format that Notion can import, or using a third-party tool that reads BibTeX and writes to Notion.

Converting BibTeX for Notion Import

Notion's database import feature accepts CSV files. The BibTeX format is not directly importable, so you need to convert the BibTeX entries into a tabular format.

The conversion process maps each BibTeX field to a column in the CSV file. The author field in BibTeX uses a specific format with names separated by the word and. You may want to keep this format as a single text string or split it into individual author names depending on how you plan to use the data.

The title field may contain curly braces in BibTeX that preserve capitalization. These braces are formatting artifacts and should be removed during conversion so the title displays cleanly in Notion.

The abstract field may contain line breaks or special characters that need cleaning. CSV files handle commas and quotes with specific escaping rules, so you need to ensure that fields containing commas are properly quoted.

You can perform this conversion using a spreadsheet application, a text editor with search and replace, or a script. The choice depends on your comfort with each tool. The goal is the same: produce a CSV file where each row is a reference and each column is a bibliographic field.

Importing References into Notion

Once you have a CSV file with your reference data, you can import it into the references database in Notion.

Create a new database in Notion with the properties you want for your references. The property names should match the column headers in your CSV file so the import maps correctly.

Use the database menu to select Import, then choose the CSV file. Notion will show you a preview of the data and allow you to adjust the property mapping before completing the import.

After the import completes, verify the record count. Compare the number of records in Notion to the number of entries in your BibTeX file. If the counts match, the import succeeded. If the counts differ, review the CSV file for formatting issues that may have caused rows to be skipped.

Check a sample of records to verify that the metadata looks correct. Look for title formatting issues, author name problems, and missing fields. Fix any issues directly in Notion or correct the CSV file and reimport.

Importing Notes into Notion

The notes import follows the same pattern as the references import, with one additional step for the relation property.

Create a notes database in Notion with properties for the note text, the relation to the references database, and any additional properties you want. The relation property must be configured before import so the notes can link to existing reference records.

Convert the CSV export from Mendeley into a format that Notion can import. The Mendeley CSV contains the note text and a reference identifier. You need to ensure that the reference identifier in the notes CSV matches the citation key or another unique identifier in your references database.

Import the notes CSV into the notes database. During the import, map the reference identifier column to the relation property. Notion will create the links between notes and references based on matching values.

Verify the import by checking that each note has a linked reference. You can create a view in the notes database that groups notes by their related reference to confirm the relationships are correct.

Creating a Custom Notion Template for Literature Notes

A template in Notion provides a consistent structure for new notes you create after the migration. The template should include the properties and layout that support your research workflow.

The template for a literature note should include the note text as the main content area. It should also include properties for the related reference, the date, and any tags you use for organizing your notes.

You can create the template by designing a new note in the notes database with the structure you want, then saving it as a template. When you create a new note, you select the template and the structure appears automatically.

The template can also include a section for your own commentary, a section for key quotes, and a section for follow-up actions. These sections help you move from passive note taking to active engagement with the literature.

The relation property in the template should be left empty for new notes. You select the related reference when you create the note, which links it to the correct source in the references database.

Using Notion Database Relations to Preserve Citation Links

The relation property is the core mechanism that preserves the connection between notes and references in Notion. Understanding how it works helps you use it effectively.

A relation property in Notion connects records in one database to records in another database. When you configure a relation between the notes database and the references database, each note can point to one or more references.

The relation creates a two-way connection. From a note, you can see the linked reference. From a reference, you can see all linked notes. This bidirectional view is useful for both reading workflows and writing workflows.

When you are reading a reference, you can see all your notes about it in one place. When you are writing and need to find a specific note, you can search the notes database and see which reference it belongs to.

The relation also enables rollup properties. A rollup property in the references database can display information from the linked notes, such as the number of notes or the date of the most recent note. This gives you an at-a-glance view of your engagement with each reference.

Practical Workflow for Ongoing Note Taking

After the migration, your workflow for new literature notes should be consistent and repeatable. The workflow has three steps: add the reference, create the note, and link the note to the reference.

When you encounter a new paper, add it to the references database first. You can do this manually by creating a new record and filling in the bibliographic details, or you can use a browser extension or citation tool that writes to Notion.

When you read the paper and want to take notes, create a new note in the notes database using your template. Write your notes in the content area, then select the related reference using the relation property.

If you need to capture a quote from the PDF, copy the text from the PDF and paste it into the note. Include the page number if you need it for citation purposes. This text-based approach replaces the highlighting workflow from Mendeley.

The advantage of this workflow is that your notes are searchable across your entire library. You can use Notion's search to find notes by topic, by reference, or by any text within the note content.

Options and Tradeoffs for Different User Types

The migration approach described here works for individual researchers, students, and small teams. Different user types may need to adjust the workflow based on their specific needs.

Graduate students writing a thesis or dissertation need to track a large number of references and notes over a long period. The two-database structure with relations supports this well because it keeps the reference library organized while allowing notes to accumulate without cluttering the reference records.

Laboratory staff managing shared literature collections need to consider collaboration. Notion supports shared databases where multiple users can add references and notes. The relation structure works the same way in a shared workspace, but you need to establish conventions for who adds references and how notes are tagged.

Researchers preparing grant applications need to connect their literature notes to the writing process. The NIH grants and funding resources describe the expectations for research proposals, and a well-organized note system helps you locate the evidence you need when writing. The ability to search your notes by topic and reference makes it easier to find supporting literature for specific sections of a proposal.

Animal owners and life-science professionals who read veterinary or biomedical literature may have smaller libraries but still benefit from the structured approach. The same export and import process works regardless of library size.

Records and Measurements for Migration Verification

Verifying the migration requires specific measurements that tell you whether the process succeeded. These measurements should be recorded before you start and checked after each step.

Record the total number of references in your Mendeley library before export. Record the total number of notes as well. These numbers are your baseline for verification.

After exporting the BibTeX file, count the number of entries in the file. This count should match your Mendeley reference count. If it does not, some references were not included in the export scope.

After converting the BibTeX to CSV and importing into Notion, count the records in the references database. This count should match the BibTeX entry count.

After importing the notes CSV, count the records in the notes database. This count should match your Mendeley note count.

Check the relation integrity by counting notes that have a linked reference. Every note should have a link. Notes without links indicate that the reference identifier in the notes CSV did not match any record in the references database.

Common Failure Patterns and How to Avoid Them

Several failure patterns recur when researchers migrate from Mendeley to Notion. Knowing these patterns helps you avoid them or recover quickly when they occur.

The first failure pattern is incomplete BibTeX conversion. The BibTeX format has quirks that do not map cleanly to CSV. Curly braces in titles, special characters in author names, and multi-line abstracts all cause problems if not handled during conversion. Inspect your converted CSV file before importing to catch these issues.

The second failure pattern is reference identifier mismatch. The CSV export from Mendeley uses an identifier that may not match the citation key in the BibTeX export. If these identifiers do not align, the relation import fails and notes end up without links. Verify the identifier format in both files before importing.

The third failure pattern is data loss from CSV escaping errors. CSV files use quotes to enclose fields that contain commas or line breaks. If the conversion tool does not handle quoting correctly, fields get split across multiple rows and the import produces corrupted records.

The fourth failure pattern is importing into the wrong database structure. If you import the references CSV into a database that lacks the expected properties, Notion may create new properties or drop data. Set up your database properties before import to match the CSV columns.

The fifth failure pattern is skipping verification. The migration appears to succeed because the import completes without errors, but the record counts do not match. Always verify counts at each step.

Limitations of the Migration Approach

The migration approach has limitations that you should understand before committing to it.

PDF annotations and highlights do not transfer. The visual markup you created in Mendeley remains in the PDF files but does not appear in Notion. If you need to reference specific passages, you must copy the text manually into your notes.

The BibTeX export does not include PDF file attachments. Your Notion references database will contain metadata but not the actual PDF files. You can add PDF attachments to Notion records manually, but this is a separate step.

Folder organization in Mendeley does not transfer. If you used folders to organize your references, you need to recreate that organization using tags or properties in Notion.

The migration is a one-time transfer, not a synchronization. Changes you make in Mendeley after the migration do not appear in Notion, and changes in Notion do not appear in Mendeley. You must choose one system as your primary tool going forward.

Safety and Data Integrity Context

Research data management involves considerations beyond the mechanics of moving files between applications. The NIH data management and sharing policy describes expectations for managing and sharing research data. While this policy applies to NIH-funded research, the underlying principles of data integrity and documentation apply to any research workflow.

Your literature notes are part of your research record. They document your reading process and your thinking about the literature. Preserving these notes with accurate metadata supports the integrity of your research process.

The Committee on Publication Ethics core practices describe expectations for authorship, data, and peer review. Proper citation and accurate attribution of sources are part of ethical research practice. A well-organized note system that preserves the link between your notes and their sources supports these practices.

When you migrate your notes, you are transferring part of your research record. The verification steps described in this article are not optional administrative tasks. They are quality controls that ensure your research record remains intact through the migration.

Professional Escalation Criteria

Most migration issues can be resolved by the individual researcher. Some situations warrant escalation to institutional support or professional assistance.

If you are migrating a large library with thousands of references and notes, consider whether the manual conversion process is reliable at that scale. A scripted conversion with automated verification may be necessary. If you do not have the technical skills to write such a script, seek help from your institution's library or research computing support.

If your notes contain sensitive or confidential information, consult your institution's data management policies before migrating to a cloud-based tool. Notion stores data on external servers, and your institution may have requirements about where research data can be stored.

If you are part of a research team with shared literature collections, coordinate the migration with your team members. A migration that works for one person may not work for the team if different members use different features of Mendeley.

If you are preparing a grant application and need to demonstrate a systematic approach to literature management, consider whether your migrated system meets the expectations described in the NIH grants and funding resources. A disorganized note system can undermine the credibility of your research plan.

Frequently Asked Questions

Can I transfer my PDF highlights and annotations to Notion?

No. The export formats from Mendeley do not include visual PDF markup. Only the text of your notes transfers. You must copy highlighted passages manually if you need them in Notion.

Will my Mendeley folder structure appear in Notion?

No. The BibTeX and CSV exports do not include folder information. You need to recreate your organizational structure using tags or properties in Notion after the import.

Do I need to keep Mendeley after migrating to Notion?

You can keep Mendeley if you still need to read PDFs and annotate them. The migration does not delete anything from Mendeley. You can use both tools, but they will not stay synchronized.

How do I know if my migration worked correctly?

Compare record counts at each step. The number of references in Mendeley should match the BibTeX entry count and the Notion reference count. The number of notes should match as well. Check that every note has a linked reference.

Can I use a third-party tool to automate the migration?

Yes. Several tools can read BibTeX files and write to Notion databases. These tools can reduce manual work, but you should still verify the results after using them.

What happens to my notes if I export only a folder instead of the whole library?

The export includes only the references and notes in the selected folder. If you export folders separately, you will need to import each export and verify that the relations work across the separate imports.

Can I add new references and notes in Notion after the migration?

Yes. The database structure supports ongoing use. Add new references to the references database and new notes to the notes database, then link them using the relation property.

Is Notion suitable for managing references for a formal publication?

Notion can organize your notes and references, but it is not a citation manager. You will still need a tool that generates formatted citations and bibliographies for your manuscript. Use Notion for your reading workflow and a citation manager for the final writing process.

Related Articles

• Biology Notes
• Two Notes Genome
• Biology Degree: Your Complete Guide to a Versatile Future
• Sample Metadata Standards for Sequencing Projects
• How to Cite Scientific Papers: A Guide to Citation Formats

References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.