Migrating to Zotero from Paperpile - best practices

bjorn · March 18, 2024

Hi all, I am going to try to migrate back from zotero from Paperpile since Zotero seems to work nicely with Obsidian.md, which is my new favorite tool. I left zotero twelve years ago, so zotero probably has evolved a lot during this time.

I though that this thread could collect ideas and observations and risks for people wanting to do this migration.

bjorn · March 18, 2024

I found these previous discussions:

https://forums.zotero.org/discussion/109286/importing-from-paperpile-how-to-reattach-pdf-attachments/p1

https://forums.zotero.org/discussion/comment/442104#Comment_442104

https://forums.zotero.org/discussion/105658/importing-ris-file-from-paperpile/p1

https://forums.zotero.org/discussion/comment/383023#Comment_383023

bjorn · May 1, 2024

This worked flawlessly using the paperpile export function.

chante77 · August 6, 2024

Bjorn, thanks for pulling these together! It seems like there are a number of ways recommended to re-attach the pdfs within these links. Which exactly did you use that worked?

THANKS!!

bjorn · September 7, 2024

I did it like this:

https://forums.zotero.org/discussion/63741/exporting-pdfs-from-paperpile#:~:text="The most convenient way turned,the RIS files is needed."

Stephanie Hallam · September 9, 2025

Does the new version of Zotero impact how migration of resources Paperpile to Zotero? What is the current process?

adamsmith · September 9, 2025

Nothing about this has changed with Zotero 7 ( nor 8 beta) so the above still applies, yes.

Karach_approves · 2025-12-01T15:44:11+00:00

Just to add to this, since this thread shows up at the top of my google search. I've used the solution mentioned by nataliatoro (here: https://forums.zotero.org/discussion/comment/383023/#Comment_383023). This was part of the thread mentioned by bjorn.

They imported the Paperpile PDFs by keeping the files in their original location, and using the "link to files in the original location" option during import.

It works great.

To then solve the issue of having my library in two locations, I selected all my files in my library and went to "Tools" > "Manage Attachments" > "Convert Linked Files to Stored Files".

This two-step solution works to copy all the files to the Zotero storage folder.

It did miss five PDFs in the end, but those are easily found if you use the option to delete the original files after converting them to stored files.