Migrating a Shared EndNote Library to Zotero

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

Quick Answer

• Export your shared EndNote library as an XML file, then import that file into Zotero to preserve reference metadata and attachment links.
• Recreate your group structure in Zotero by creating groups and inviting collaborators before transferring references into shared collections.
• Verify permissions and sync settings after migration because Zotero group libraries have different sharing rules than EndNote shared libraries.

Understanding the Migration Context

Teams choose to move from EndNote to Zotero for several practical reasons. Zotero offers open source access, browser-based capture, and group libraries that support real time collaboration. The migration process itself is straightforward for individual libraries, but shared libraries introduce complications around folder structure, attachment handling, and permission settings.

The core challenge is not exporting and importing references. That process works reliably. The challenge is preserving the organizational structure that your team built over time and re-establishing the collaboration rules that governed who could see and edit which references.

Before you begin, confirm that every team member has completed their pending edits in EndNote. Exporting a library while someone is actively editing can produce incomplete records. Ask each collaborator to close the shared library and confirm they have synced their local changes.

At a Glance

Preparing Your EndNote Library for Export

Audit the Library Before Export

Open your shared EndNote library and review the reference count. Compare this number against your team's records to confirm nothing is missing. Check for duplicate references, incomplete records, and orphaned attachments. Cleaning the library before export reduces the amount of manual work required after import.

Review your group structure in EndNote. Write down the names of every group and smart group, and note the hierarchy if you use nested groups. Zotero does not import EndNote group structures automatically, so you will need to recreate these collections manually.

Check Attachment Storage Settings

EndNote stores attachments either in the library file itself or in a separate folder. Open Edit > Preferences > Folder Locations to see where your PDFs and other files are stored. If attachments live in a folder, you must copy that folder alongside your exported XML file.

Decide whether you want Zotero to store copies of attachments or link to existing files. Storing copies creates a self-contained Zotero library that is easier to sync across devices. Linking to files keeps your current folder structure but requires all team members to have access to the same file paths.

Export the Library as XML

In EndNote, select File > Export. Choose the XML format instead of RIS or plain text. XML preserves more fields, including notes, abstracts, and custom field data. Name the file clearly and save it to a location your team can access.

For shared libraries, export the entire library instead of individual groups. This ensures you capture every reference even if some references are not assigned to a group. You can sort references into collections after import.

Importing into Zotero

Create Your Zotero Account and Install the Desktop App

Each team member needs a Zotero account before migration begins. The account enables sync and group library access. Install the Zotero desktop application on each computer that will participate in the shared library.

The Zotero account also connects to ORCID, which allows researchers to maintain a persistent identifier for their published work. This integration is useful for teams that track authorship and publication records across projects.

Import the XML File

Open Zotero desktop and select File > Import. Choose the XML file you exported from EndNote. Zotero will create a new collection named after the file and populate it with your references.

Review the imported references for metadata errors. Check author names, publication dates, journal titles, and DOI fields. EndNote and Zotero handle some fields differently, so minor formatting differences are common. Correct these issues before moving references into shared collections.

Handle Attachments During Import

Zotero will import attachment links from the XML file. If your attachments were stored in an EndNote folder, you must ensure that folder is accessible from each computer that will use the library. Alternatively, you can reattach PDFs manually after import.

For teams that want a fully synced library, use Zotero's Store Copy option when adding attachments. This places a copy of each file in Zotero's storage and syncs it across all devices. Storage limits apply, so check your Zotero storage allocation before uploading large PDF collections.

Rebuilding Folder Structure in Zotero

Create Collections That Mirror Your EndNote Groups

Zotero uses collections instead of groups to organize references within a library. Create collections that match the group names from your EndNote library. If you used nested groups, create subcollections to preserve that hierarchy.

Drag references from the imported collection into their appropriate collections. This manual step is necessary because Zotero does not read EndNote group assignments from the XML file. Plan for this work and assign it to one person to avoid duplication.

Use Tags for Cross-Cutting Organization

If your EndNote library used groups for cross-cutting categories such as project status or manuscript stage, consider using Zotero tags instead. Tags can be applied to references across multiple collections and are searchable. This approach reduces the need for duplicate references in multiple collections.

Zotero allows a reference to exist in multiple collections simultaneously. This differs from EndNote groups, which also allow multiple group membership. Use this feature to maintain flexible organization without duplicating records.

Re-Establishing Group Permissions and Sync Settings

Create Zotero Groups for Collaboration

Zotero groups function as shared libraries with their own permission settings. Create a group for your team and choose the membership and access level that matches your collaboration model. Group libraries appear separately from your personal library in the Zotero interface.

Invite team members to the group using their Zotero account email addresses. Each member must accept the invitation before they can access the group library. Confirm that every collaborator has accepted their invitation before you begin moving references.

Assign Roles Based on Team Needs

Zotero group roles control what each member can do within the group library. The group owner manages settings and membership. Members can add and edit references. Readers can view references but cannot make changes.

Match these roles to your team's previous EndNote permissions. If some collaborators had read only access in EndNote, assign them the Reader role in Zotero. If everyone could edit, assign Member roles. Review these assignments periodically as team membership changes.

Configure Sync Settings on Each Computer

Each team member must enable sync in their Zotero desktop application. Open Edit > Preferences > Sync and enter the Zotero account credentials. Select the option to sync group libraries automatically.

Sync settings determine how quickly changes appear for all collaborators. Zotero syncs continuously when the desktop application is open. Team members who work offline will sync their changes when they reconnect to the internet.

Practical Implementation Steps

Step 1: Schedule the Migration Window

Choose a time when the team is not actively writing or editing manuscripts. Confirm that all pending changes are saved in EndNote. Notify the team that the shared library will be unavailable during migration.

Step 2: Export and Verify the XML File

Export the EndNote library as XML. Open the file in a text editor and confirm it contains the expected number of references. Check that attachment file paths are present and point to accessible locations.

Step 3: Import and Audit in Zotero

Import the XML file into Zotero. Compare the reference count in Zotero against the EndNote count. Spot check records for metadata accuracy. Resolve any discrepancies before proceeding.

Step 4: Create Collections and Groups

Create the collection structure that mirrors your EndNote groups. Create the Zotero group and invite team members. Assign roles based on your permission plan.

Step 5: Move References and Attachments

Drag references from the imported collection into their target collections. Verify that attachments are linked or stored correctly. Test that PDFs open from Zotero on multiple computers.

Step 6: Test Collaboration Features

Ask two team members to add a test reference to the group library simultaneously. Confirm that both members see the new reference after sync. Test editing permissions by having a Reader attempt to modify a reference and confirming they cannot.

Step 7: Retire the EndNote Library

After the team confirms Zotero is working correctly, archive the EndNote library. Keep the exported XML file as a backup. Do not delete the EndNote library until the team has used Zotero for at least one full project cycle.

Records and Measurements

Track Migration Progress

Create a simple spreadsheet to track migration tasks. List each EndNote group, the corresponding Zotero collection, and the person responsible for moving references. Record the date each collection was completed and verified.

Measure Reference Integrity

After import, run a duplicate check in Zotero. Zotero can identify potential duplicates based on title, DOI, or other fields. Record the number of duplicates found and resolved. This measurement tells you whether your EndNote library had hidden duplication issues.

Document Permission Assignments

Maintain a record of which team members have which roles in the Zotero group. Update this record when team members join or leave. This documentation supports accountability and helps new members understand their access level.

Common Failure Patterns

Broken Attachment Links

The most common migration failure is broken attachment links. This happens when the EndNote attachment folder is not copied alongside the XML file, or when file paths change after migration. Test attachments on every team member's computer to catch this early.

Lost Folder Structure

Teams often expect Zotero to import EndNote group structures automatically. This does not happen. If you skip the manual collection creation step, references arrive in a single flat collection with no organization. Allocate time for this manual work.

Permission Confusion

EndNote shared libraries and Zotero group libraries handle permissions differently. Team members who had full access in EndNote may find themselves with limited access in Zotero if roles are assigned incorrectly. Review role assignments with each team member after migration.

Sync Conflicts

When multiple team members edit the same reference simultaneously, Zotero may create conflicting versions. Zotero resolves these conflicts by keeping both versions and flagging the conflict. Train the team to check for conflict warnings after sync.

Incomplete Metadata

EndNote fields do not always map cleanly to Zotero fields. Custom fields, notes, and some abstract formatting may not transfer perfectly. Plan a metadata review pass after import to catch and correct these issues.

Welfare and Safety Context

Data Integrity for Research Teams

Research teams have an obligation to maintain accurate reference records. The Committee on Publication Ethics core practices emphasize the importance of data integrity and proper record keeping in research. A poorly executed migration that loses references or corrupts metadata can undermine the integrity of the research record.

Compliance with Funding Requirements

Teams receiving NIH funding must comply with the NIH Data Management and Sharing Policy. This policy expects researchers to manage and share data according to a documented plan. Reference libraries are part of the research data ecosystem, and migration should preserve the integrity of these records.

Author Identity and Attribution

ORCID provides persistent identifiers that distinguish researchers with similar names. When migrating reference libraries, confirm that author identifiers are preserved or reattached in Zotero. This supports accurate attribution and reduces the risk of misidentifying authors in collaborative projects.

Transparent Reporting Standards

The EQUATOR Network promotes transparent and accurate reporting in research. Proper citation management supports this goal by ensuring that references are complete and verifiable. A migration that introduces citation errors can compromise the transparency of future publications.

Limitations and Professional Escalation

When to Seek Technical Support

If the XML export fails repeatedly, or if the imported file contains corrupted records, stop the migration and seek support. Zotero forums and EndNote technical support can provide guidance. Do not attempt to manually repair a corrupted XML file without expert assistance.

When to Involcthe Team Lead

If team members cannot agree on the collection structure or permission model, escalate to the team lead before proceeding. Rebuilding the structure after migration is more time consuming than resolving disagreements beforehand.

When to Consult Institutional Research Support

Institutions often have research support offices that assist with reference management. If your team lacks the technical expertise to complete the migration, consult these offices. They may offer training, templates, or direct assistance.

When to Reconsider the Migration

If your team relies heavily on EndNote features that Zotero does not provide, reconsider the migration. Zotero does not support all EndNote features, including some advanced manuscript formatting options. Evaluate your team's specific workflow before committing to the migration.

Decision Framework for Choosing Between Full Migration and Hybrid Operation

Assess Your Team's Readiness Before Committing

A full migration from EndNote to Zotero is not the right choice for every team at every moment. Some teams benefit from a hybrid period where both systems operate in parallel. Others should complete the migration in one focused window. The decision depends on three factors: active project deadlines, team technical comfort, and the complexity of your existing library structure.

Start by listing every active manuscript, grant application, and literature review that depends on the shared EndNote library. Assign a completion date to each item. If any project has a submission deadline within the next four weeks, a hybrid operation may be safer than a full cutover. Teams that attempt a full migration during peak writing periods often find themselves reverting to EndNote mid migration, which creates two divergent libraries and doubles the cleanup work later.

Evaluate Technical Comfort Across the Team

Survey each team member about their experience with Zotero. Do not assume that familiarity with EndNote translates to Zotero competence. The two tools use different mental models for organization. EndNote groups feel like folders. Zotero collections behave more like tags that can hold the same reference in multiple places simultaneously. Team members who struggle with this conceptual shift will need training time built into the migration schedule.

Identify one person who will serve as the migration lead. This person should have completed a test migration with a small sample library before the team begins. The migration lead handles the export, the import, the collection structure, and the group permission setup. Other team members focus on verifying their own references and learning the Zotero interface. Distributing the work this way prevents the common failure pattern where everyone assumes someone else is managing the migration.

Compare Library Complexity Against Migration Effort

Count the number of groups, smart groups, and nested groups in your EndNote library. Write this number down. Then estimate how many of those groups represent active organizational logic versus legacy structure. Teams often discover that a significant portion of their EndNote group structure is outdated. Groups created for projects that ended years ago still appear in the library. The migration is an opportunity to archive or delete these stale groups instead of recreate them in Zotero.

For libraries with fewer than 20 active groups, a direct migration with manual collection recreation is straightforward. For libraries with more than 50 groups, consider whether your team actually uses that level of granularity. If team members primarily search by keyword or author instead of browsing groups, a flatter collection structure with robust tagging may serve the team better. This decision reduces the manual work of recreating collections and makes the Zotero library easier to navigate.

Choose Between Full Cutover and Parallel Operation

A full cutover means the team stops using EndNote on a specific date and uses only Zotero from that point forward. This approach works best when the team has no imminent deadlines, everyone has completed basic Zotero training, and the library is well organized. The advantage is a single source of truth. The risk is that unresolved EndNote workflows force the team to reopen the old library.

A parallel operation means the team keeps EndNote available for reference while gradually moving active projects into Zotero. This approach suits teams with imminent deadlines or members who need more time to learn Zotero. The critical rule for parallel operation is that no reference is edited in both systems. Assign each active project to one system and enforce that assignment. When a project completes, move its references into Zotero and mark the EndNote group as archived.

Establish a Rollback Decision Point

Before you begin the migration, define the conditions that would cause the team to stop and return to EndNote. Write these conditions down and share them with the team. Examples include losing more than 5 percent of references during import, discovering that critical attachment files are inaccessible, or finding that team members cannot sync group libraries within two days of setup.

Set a specific date to evaluate these conditions. For most teams, the third day after the initial import is the right checkpoint. By that point, the team has had time to test attachments, verify metadata, and attempt collaborative edits. If the rollback conditions are met, restore the EndNote library from the archived backup and document what went wrong. This decision point gives the team permission to stop without treating the migration as a failure. A controlled rollback is less damaging than a chaotic abandonment of Zotero weeks later.

Document the Decision and Assign Accountability

Create a one page migration decision record that states the chosen approach, the reasons for that choice, the rollback conditions, and the migration lead name. Share this record with the team before the migration begins. The record serves two purposes. It aligns expectations about how the migration will proceed, and it provides a reference point if disagreements arise later about whether the team committed to a full cutover or a hybrid operation.

The migration lead updates this record at each checkpoint. The record becomes part of the team's project documentation and supports the data integrity expectations described in the Committee on Publication Ethics core practices. Accurate documentation of the migration decision and its outcomes also supports compliance with the NIH Data Management and Sharing Policy, which expects researchers to maintain clear records of how research data and associated materials are managed.

Match the Decision Framework to Your Team Size

Small teams of two to five people can usually complete a full cutover within a few days. The migration lead can personally verify every reference and attachment. Communication is simple because the entire team can meet in one session to review the imported library.

Medium teams of six to fifteen people benefit from a structured hybrid approach. Assign each team member responsibility for verifying references in their own research area. The migration lead coordinates the collection structure and group permissions. Schedule two verification sessions where team members report discrepancies and the migration lead resolves them.

Large teams with multiple research groups should treat the migration as a project with phases. Migrate one research group at a time. Confirm that group is working correctly in Zotero before moving the next group. This phased approach limits the blast radius of any single migration error and gives later groups the benefit of lessons learned from earlier groups.

Use the Decision Framework to Prevent Common Failures

The most common migration failure is not technical. It is organizational. Teams that skip the readiness assessment often discover mid migration that some members are not prepared to switch systems. The decision framework forces the team to confront these issues before the export begins.

Teams that choose a full cutover without checking deadlines often find themselves unable to access references during a critical writing period. The decision framework prevents this by requiring a deadline audit before the migration starts.

Teams that choose a hybrid operation without assigning projects to specific systems often create duplicate references across both tools. The decision framework prevents this by requiring explicit project assignments and a rule against editing the same reference in both systems.

Record the Migration Outcome for Future Reference

After the migration reaches the rollback decision point, record the outcome in the migration decision record. Note the reference count before and after migration, the number of attachments verified, the number of duplicates found and resolved, and any references that required manual correction. This record becomes a template for future migrations, whether the team moves to a different tool or onboard new team members who need to understand how the Zotero library is organized.

The record also supports the transparent reporting standards promoted by the EQUATOR Network. When the team publishes research that relied on the migrated library, the migration record demonstrates that reference integrity was maintained through the transition. This documentation is especially valuable for teams that face audit requirements from funders or institutions.

Frequently Asked Questions

Can I migrate a shared EndNote library to Zotero without losing references?

Yes, you can migrate without losing references if you export the complete library as XML and verify the reference count after import. The XML format preserves more metadata than other export formats. Confirm that every team member has synced their changes before exporting.

Will my EndNote folder structure carry over to Zotero automatically?

No, Zotero does not import EndNote group structures. You must create collections in Zotero manually and move references into them. Plan for this manual work and assign it to one person to avoid duplication.

How do I handle PDF attachments during migration?

You can either link to existing PDF files or store copies in Zotero. Storing copies enables sync across devices but consumes storage. Linking preserves your current file structure but requires all team members to access the same file paths.

What are the differences between EndNote shared libraries and Zotero group libraries?

EndNote shared libraries use a single library file that multiple users access. Zotero group libraries are separate libraries that sync through Zotero servers. Zotero groups have distinct roles for owners, members, and readers, while EndNote sharing is less granular.

How long does the migration take for a typical research team?

The time depends on library size and team coordination. Export and import take minutes, but rebuilding collections and verifying metadata can take several hours. A team with a few thousand references should plan for one to two days of focused migration work.

Can team members use Zotero while the migration is in progress?

Team members can use Zotero for their personal libraries during migration, but the shared group library should not be used until migration is complete. Using the group library before references are moved creates confusion about which references are authoritative.

What should I do if some references fail to import?

Compare the reference count between EndNote and Zotero to identify missing records. Re-export the EndNote library and try the import again. If specific references consistently fail, check those records for corrupted fields or unusual characters.

Do I need to keep the EndNote library after migration?

Keep the EndNote library and the exported XML file as backups until the team has used Zotero for at least one full project cycle. This backup protects against unexpected data loss and gives the team a fallback option if Zotero does not meet expectations.

Using the Evidence

Related Articles

• Reference Managers for Researchers: Choosing a Workflow That Survives Collaboration
• Genomic Library
• Ncbi Reference Genome
• Qpcr Reference Gene Validation
• Single Cell Reference Mapping

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.