How to export your ReadCube Papers library (and what doesn't come with it)

Q: How do I export my ReadCube library?

Select all references in your ReadCube library with Cmd-A or Ctrl-A , right-click the selection, and choose Export to > RefMan (.ris) . This creates an RIS file containing your reference metadata. Your PDFs are not included in it.

By Suzanne O’Regan · Published Oct 6, 2026 · Updated Oct 7, 2026

ReadCube (previously called Papers) lets you export your reference metadata to a standard bibliography file. Your PDFs must be transferred separately. Standard bibliography formats do not preserve collections, PDF annotations, or application-specific information such as tags and reading status. What you can import will depend on the reference manager you are moving to.

Quick answer: In ReadCube, select all references using Cmd-A on macOS or Ctrl-A on Windows. Right-click the selection and choose Export to > RefMan (.ris). To export PDFs, select all references, right-click the selection and choose Export to > PDF. Keep the RIS file together with your folder of PDFs.

What you can and can’t export from ReadCube (Papers)

A standard RIS or BibTeX export carries bibliographic information, not your complete ReadCube library. PDFs need to be exported separately.

What a standard reference export transfers out of ReadCube

Content	Included in bibliography file export?	Notes
Reference metadata	Yes	Includes fields such as authors, titles, journals, publication dates, and DOIs. Some values may require correction after import.
PDFs	No	PDFs remain in your ReadCube library folder and must be exported separately.
Collections and folder structure	No	Standard bibliography formats do not preserve collections or folders.
PDF annotations and highlights	No	Application-managed annotations are not represented in RIS or BibTeX. Annotations embedded in PDFs may remain visible.
Labels, reading status, flagged papers, and other ReadCube-specific data	No	These fields generally have no equivalent in standard bibliography formats.

Export your references from ReadCube

You will need to export your references to a bibliographic file. In your ReadCube library:

Select all references using Cmd-A on macOS or Ctrl-A on Windows.
Right-click the selection.
Choose Export to > RefMan (.ris).

The RIS format is supported by most reference managers, including Paperpile, Zotero, EndNote, and Mendeley.

BibTeX may also be suitable if your preferred reference manager supports it.

Export or locate your ReadCube (Papers) PDFs

The RIS file contains bibliographic metadata, such as titles, authors, journals, and publication dates. It does not contain the PDF files attached to your references.

You have two ways to transfer your PDFs.

Option 1: Export your PDFs in bulk

You can export the PDFs from your ReadCube library (ReadCube desktop app v5 and web app):

Select all references using Cmd-A on macOS or Ctrl-A on Windows.
Right-click the selection.
Choose Export to > PDF.
Save the files in a dedicated folder.

Depending on the destination application, you may be able to import this folder, search it for matching PDFs, or attach the files manually after importing your references.

Option 2: Use your Papers library folder (legacy desktop app v4.0 only)

If you have the legacy desktop app (v4.0) installed and you have synced your library offline, your PDFs are stored in the Papers library folder on your computer.

Some reference managers can use this folder during migration or attempt to match its files to your imported references. Keep the folder structure intact until you know how your destination application will handle the files.

Before importing your ReadCube (Papers) library to another reference manager

Keep the exported folder of PDFS together with the exported bibliography file on your computer until you have:

Imported the library into the new application.
Checked a sample of your reference metadata for missing details.
Confirmed that important references are available in the new application.

Import your ReadCube (Papers) library into Paperpile

Paperpile has a migration assistant specifically for ReadCube Papers. It accepts both the RIS file containing your reference metadata and the ReadCube library folder containing your PDFs.

To use it:

Export your ReadCube references as a RIS file.
Locate the ReadCube library folder on your computer.
In Paperpile, open the Add menu.
Choose Import from other programs > ReadCube Papers.
Add the RIS file and the ReadCube library folder to the upload dialog.
Start the import and review the results.

The migration assistant matches the PDFs in the library folder to their corresponding references. After the import, you can filter for references marked as incomplete and merge duplicates.

Import your ReadCube (Papers) library into Zotero

Zotero does not have a dedicated ReadCube importer. Its migration documentation recommends exporting references to a standardized format such as RIS, BibTeX, or CSL JSON.

To import your RIS file:

Export the references from ReadCube as a RIS file.
In Zotero, choose File > Import…
Select A file.
Choose the exported RIS file and complete the import.
Attach your PDFs separately by dragging and dropping them into an empty space in the center pane of your Zotero library. Zotero will attempt to match the PDFs to their bibliographic items.

The imported items will not automatically include your ReadCube collections. After importing, check publication dates, special characters, and a selection of frequently used references.

Import your ReadCube (Papers) library into EndNote

EndNote supports the RIS bibliography format. The general migration process is:

Export your references from ReadCube as a RIS file.
In EndNote, choose File > Import > Show Options.
In the Import Options menu, choose Reference Manager (RIS).
Select the exported RIS file and let the import finish.
Attach the PDFs separately.
Reconstruct any lists or folder structure you want to retain.
Review a sample of the imported metadata.

Import your ReadCube (Papers) library into Mendeley

Method 1: Import reference metadata

Mendeley supports standard bibliography formats such as RIS. The general migration process is:

Export your references from ReadCube as an RIS file.
In Mendeley, click Add references > Import file(s).
Choose the RIS file and allow the import to finish.
Attach your PDFs one-by-one. To attach a PDF to a reference, double click on any reference to open its metadata panel, then click the plus button next to Files.
Recreate any organizational structure you want to retain.
Review a sample of the imported metadata.

This works well if you only need the reference metadata in Mendeley or have just a few PDFs in your ReadCube library that you need to transfer over.

Method 2: Import a folder of PDFs

If you have a large library of PDFs that you need to move, you can import a folder of your PDFs instead:

On your computer, find the ReadCube folder with your PDFs.
In Mendeley, click Add references > Import folder(s).
Select the folder and allow the import to finish.
Mendeley will attempt to automatically get the metadata for your PDFs, but make sure to review a sample of your references.

Check your reference metadata after importing

Reference metadata may be interpreted differently when transferred between applications. Users who have migrated from ReadCube to Zotero have reported issues including:

Apostrophes appearing as HTML entities.
Ampersands, quotation marks, and the > symbol importing incorrectly.
Inconsistent handling of Greek letters and other special characters.
Italics being removed from titles.
Publication years being omitted from some RIS exports, as reported in a 2024 Zotero discussion.

After importing, check a sample of references containing:

Apostrophes, ampersands, or quotation marks in author, title, or publisher fields.
Greek letters, mathematical symbols, or italicized terms.
Incomplete publication dates.
Older references that may previously have been imported from another application.
Frequently used or particularly important papers.

You can also sort the imported library by year to identify missing or incorrect dates and search for a few titles that contain special characters.

Tip: Paperpile automatically detects incomplete references via a filter menu, and lets you automatically update missing reference information.

Rebuild your ReadCube (Papers) collections

Collections and folder structures are not included in standard RIS or BibTeX exports. You will need to recreate this organizational structure in the destination application.

Before leaving ReadCube, record your existing collections. You could take screenshots, write down the collection names, or create a simple list.

After importing, you can either:

Recreate the collections in your new reference manager and move the relevant references into them.
Use labels, tags, or filters to rebuild collections based on information already stored in the reference metadata, such as keywords, authors, or journals.

Compare reference managers

If you are still choosing where to move your library, see:

Frequently Asked Questions about exporting from ReadCube

How do I export my ReadCube library?

Select all references in your ReadCube library with Cmd-A or Ctrl-A, right-click the selection, and choose Export to > RefMan (.ris). This creates an RIS file containing your reference metadata. Your PDFs are not included in it.

Does exporting from ReadCube include my PDFs?

No. A bibliography file export contains citation metadata rather than the PDF files themselves. Your PDFs need to be exported separately. Depending on the reference manager you are moving to, you may be able to provide this folder during import, use a PDF-matching feature, or attach the files manually.

Will my lists, collections, and folders transfer?

No. Collections are not included in any standard exchange format such as RIS or BibTeX, so they are not recorded in the export regardless of which reference manager you move to. You will need to recreate your organizational structure in the destination application.

Can I export my annotations from ReadCube?

RIS and BibTeX do not contain fields for highlights or PDF annotations. Annotations embedded directly in a PDF may remain visible when the PDF is opened in another application. Annotations stored separately by ReadCube may not transfer with either the bibliography file or the PDF.

How do I move my ReadCube library to Zotero?

Export your references from ReadCube as a RIS file. In Zotero, choose File > Import… > A file, then select the exported file. Zotero does not have a ReadCube importer, so importing PDFs will require additional steps. After importing, check publication dates, special characters, and a selection of frequently used references.