Published Jan 20, 2025 ⦁ 14 min read
The Top 10 Alternatives to Mendeley in 2025

The Top 10 Alternatives to Mendeley in 2025

With Mendeley losing favor due to limited free storage and discontinued mobile apps, researchers are turning to better tools for managing references. Here’s a quick list of the top 10 Mendeley alternatives in 2025 to streamline your academic workflow:

  • Paperpile: Unlimited storage, Google Docs integration, $2.99/month.
  • Zotero: Free, open-source, 300MB free storage, optional upgrades.
  • EndNote: Advanced features, $125 one-time fee.
  • Qiqqa: Offline PDF management, free basic version.
  • Docear: Mind-mapping for research, free and open-source.
  • BibDesk: macOS-specific, integrates with LaTeX, free.
  • ReadCube Papers: Cloud storage, smart organization, $5/month.
  • Citavi: Research planning tools, starts at $89/year.
  • RefWorks: Unlimited cloud storage, institutional access available.
  • Sourcely: AI-powered, free and premium options.

Quick Comparison

Tool Price Storage Key Feature Best For
Paperpile $2.99/month Unlimited Google Docs integration Cloud users
Zotero Free 300MB (free tier) Open-source flexibility Students
EndNote $125 (one-time) Unlimited (premium) Advanced citation tools Research professionals
Qiqqa Free Local storage Offline PDF management Offline users
Docear Free Local storage Mind-mapping organization Visual thinkers
BibDesk Free Local/iCloud macOS Spotlight search Mac users
ReadCube Papers $5/month 10GB (free tier) Smart folders, annotations Publishers
Citavi $89/year Cloud sync Task assignments Collaborative teams
RefWorks Institutional Unlimited Real-time collaboration Academic institutions
Sourcely Free/premium Unlimited (paid) AI-powered source analysis AI enthusiasts

Ready to find the right tool for your research? Let’s explore their features and differences in detail.

Reference Managers: Everything You Need to Know About EndNote, Mendeley, and Zotero

EndNote

1. Paperpile: A Modern Reference Manager

Paperpile

Paperpile is a cloud-based tool designed to simplify how researchers organize and manage their academic references. Its user-friendly design and cloud functionality cater to the increasing need for tools that make academic workflows easier.

Unlike Mendeley, Paperpile offers seamless platform integration and has dedicated mobile apps for both Android and iOS. It works smoothly with Microsoft Word and Google Docs, making citation management hassle-free. A survey of 733 users revealed that 59% of Paperpile users had previously used Mendeley, highlighting its growing appeal.

At just $2.99 per month, Paperpile provides unlimited storage and full access to its features, making it a more budget-friendly option compared to Mendeley's pricing tiers. Here's a quick comparison:

Feature Paperpile Mendeley
Storage Unlimited ($2.99/mo) 2GB (Free), 5GB ($4.99/mo)
Mobile Apps Android & iOS None
Google Docs Integration Yes No
Real-time Collaboration Yes Limited

Paperpile also includes tools for annotating and highlighting PDFs, with instant syncing across devices. This makes collaborative research more efficient, as notes and annotations are updated in real time for teams.

Security is another priority for Paperpile, ensuring compliance with key regulations to keep research data safe during storage and sharing.

With its combination of modern features, ease of use, and affordable pricing, Paperpile is a strong choice for researchers looking for a cloud-based reference manager. Up next, we'll take a closer look at Zotero, a free and open-source option.

2. Zotero: A Free and Open-Source Option

Zotero is a strong alternative to Mendeley, especially for those looking for a no-cost solution with plenty of features. It’s completely free to use, with optional low-cost storage upgrades.

It works smoothly with tools like Microsoft Word, LibreOffice, Google Docs, and LaTeX (via BibTeX), offering flexibility that Mendeley may not always match [1][2].

With tagging and annotation tools, Zotero makes managing and organizing PDFs straightforward, simplifying the review process [1].

Here’s a quick look at Zotero’s storage plans:

Storage Plan Space Annual Cost Features
Free Tier 300 MB $0 Unlimited citations, Full functionality
Basic Storage 2 GB $20 Cloud sync, Backup
Premium Storage 6 GB $60 Priority support

Collaboration is another area where Zotero shines. It allows real-time library sharing, making it perfect for research teams and academic groups. Shared collections can be created, and team members can work on projects simultaneously, with updates syncing instantly across devices [1].

Zotero supports over 9,000 citation styles, offering compatibility with nearly any academic journal or institution. Its web-based interface ensures you can access your references from any device, eliminating the need for desktop-only software.

As an open-source platform, Zotero benefits from a community-driven model that ensures regular updates and strong support from its user base [1].

While Zotero offers affordability and flexibility, Endnote provides a more all-encompassing approach to managing research.

3. Endnote: A Research Management Tool

Endnote is a reference management tool known for its integration capabilities and advanced features. It's designed with professionals and institutions in mind, making it ideal for managing large-scale research projects. Many universities offer institutional subscriptions, giving members full access [2].

The tool works well with popular platforms like Microsoft Word, Google Docs, Apache OpenOffice, and Pages. With its built-in PDF annotation feature, users can highlight text and add notes directly to documents, simplifying the review process [4].

Here’s a quick look at what Endnote offers:

Feature Category Capabilities
Platform Support Windows, Mac, iPad, iPhone
Storage Unlimited (Premium Plan)
Integration MS Word, Google Docs, OpenOffice
Citation Styles Wide range of citation styles
Mobile Access Native iOS apps

Endnote also includes helpful features like journal abbreviation recognition and an automatic bibliography ordering system, which make citation formatting much easier [2]. Its online platform supports shared libraries, allowing teams to collaborate on documents in real-time [2].

The tool is available for a one-time purchase of $125, which includes unlimited storage - a great option for dedicated researchers [5]. Mobile access is supported via iOS apps and cloud syncing, though the lack of Linux compatibility may be a drawback for some users [2][5].

For those looking for a more visual way to manage references, Qiqqa might be worth exploring.

4. Qiqqa: A Research Management Solution

Qiqqa

Qiqqa stands out by focusing on local document management instead of relying on cloud-based storage. This makes it a solid choice for users who prefer offline workflows. It helps researchers stay organized by allowing them to tag, categorize, and annotate PDFs, which is especially useful during literature reviews.

Here’s a quick look at what Qiqqa offers:

Feature Category Capabilities
Document Management Organize PDFs, tagging, and search tools
Annotation Tools Highlight text, add notes, and underline
Integration Works with Microsoft Word, Google Docs, and BibTeX
Collaboration Shared libraries and real-time commenting
Backup Local backups for easy PC transfer
Cost Free version with essential features

Qiqqa integrates with Microsoft Word, Google Docs, and supports BibTeX, making citation management smooth across various writing platforms. Its shared library and real-time commenting features also make it easier for teams to collaborate on local networks.

The free version of Qiqqa provides access to its core features, making it a great option for researchers on a tight budget. However, its duplicate detection is limited to references and doesn’t check actual document content. Plus, since there’s no cloud storage, users need to handle backups manually, which might not suit everyone.

For those who prioritize managing PDFs offline, Qiqqa is a practical choice. While Qiqqa shines in local document handling, tools like Docear bring something different to the table with their mind-mapping approach to organizing references.

5. Docear: A Mind-Mapping Reference Manager

Docear

Docear blends mind-mapping with reference management, offering a visual way to organize academic research. Its system is particularly useful for structuring literature reviews and thesis work by mapping out research hierarchies. Built on the Freeplane platform, it enhances traditional mind mapping with academic-focused tools.

Feature Description
Mind Mapping & Citations Visual organization with multiple citation styles
PDF Management Links annotations directly to mind maps
Platform Support Available on Windows, macOS, and Linux
Cost Free and open-source
Collaboration Shared mind maps for team projects

One standout feature is its ability to connect PDF annotations directly to references in mind maps, simplifying the process of organizing notes. By visualizing relationships between sources, users can easily spot gaps in their research.

Although the interface might feel overwhelming for beginners, its no-cost, open-source model makes it appealing for those on a tight budget. Docear also integrates with popular word processors, allowing for smooth citation management. Its visual focus is particularly helpful for managing complex research projects.

For Mac users looking for an Apple-specific option, BibDesk provides a more streamlined alternative.

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6. BibDesk: A Mac-Based Reference Tool

BibDesk

BibDesk is a free, open-source reference manager designed specifically for macOS users. It takes full advantage of Apple's ecosystem, making it a go-to option for academics and researchers who rely on Mac devices.

One of BibDesk's standout features is its integration with macOS Spotlight, allowing you to quickly search through your reference library. Its iCloud sync ensures your research stays updated across all Apple devices. For those working with LaTeX, BibDesk's built-in BibTeX support makes it an excellent choice compared to more general-purpose tools.

Feature Description
Integration Built-in support for BibTeX and LaTeX editors
Storage Local storage with optional iCloud sync
Search macOS Spotlight integration for fast searches
Security Local data storage with optional cloud backup
Cost Free and open-source

BibDesk makes it easy to download and manage PDFs, add annotations, and store notes directly alongside your references. This setup streamlines your workflow and keeps everything in one place. The tool also supports various citation styles and allows you to export bibliographies in multiple formats, catering to different publication needs.

For those migrating from other tools, BibDesk supports imports from RIS and EndNote formats. Its local-first storage approach, with optional cloud backup, gives you greater control over sensitive research data.

Thanks to its community-driven development, BibDesk receives regular updates based on user feedback. While it excels in macOS integration, some users may prefer alternatives like ReadCube Papers for broader research library organization - more on that next.

7. ReadCube Papers: A Research Library Organizer

ReadCube Papers

ReadCube Papers connects with Google Drive, Dropbox, OneDrive, and institutional repositories, offering easy access to research materials across devices. Its PDF tools let you highlight, add sticky notes, and make detailed annotations directly within documents. Managing large collections is straightforward with its tagging and folder setup.

Feature Description
Cloud Integration Works with Google Drive, Dropbox, and institutional repositories
Annotation Tools Highlighting, sticky notes, and collaborative comments
Organization Smart folders, custom tags, and automated metadata management
Pricing Free version available; Premium: $5/month (billed annually)
Mobile Access Apps available for iOS and Android

Teams can share libraries, collaborate on annotations, and hold real-time discussions within the platform. This makes it a great tool for group research projects.

The smart search feature helps you find articles quickly from your library or connected repositories. It also integrates directly with major academic databases like PubMed, arXiv, and CrossRef.

For citation management, ReadCube Papers works with EndNote and Zotero and supports various citation styles. The free version handles basic tasks, while the premium plan offers more advanced options for $5/month (billed annually).

Next, we'll look at how Citavi aids in research planning and writing.

8. Citavi: A Tool for Research and Writing

Citavi

Citavi goes beyond the capabilities of tools like Mendeley by combining reference management with advanced features for organizing knowledge. It integrates smoothly with Microsoft Word and Google Docs, offering automatic citation detection to simplify both writing and referencing.

This platform includes powerful PDF annotation tools such as highlighting, sticky notes, and categorization, all of which sync automatically across devices. Citavi also supports team research with features like real-time commenting, shared projects, and task assignments, making it a strong choice for collaborative work.

Feature Capability
Document Management PDF annotation, highlighting, categorization
Integration Microsoft Word, Google Docs, major databases
Collaboration Real-time commenting, shared projects, task assignment
Data Import/Export Supports BibTeX, RIS, and CSV formats
Cloud Access Synchronization across devices

Citavi is available in a free version, with premium licenses starting at $89 per year, and team plans tailored for institutions.

One of its most impressive features is the automatic citation detection, which accurately extracts citations from PDFs. Citavi also allows users to customize data fields and import references from a variety of academic databases. Its intuitive organization system helps users categorize and retrieve information with ease, making it especially useful for large-scale literature reviews.

For those looking for a fully cloud-based option with strong academic tools, RefWorks is another solid alternative to consider.

9. RefWorks: A Cloud-Based Reference Manager

RefWorks

RefWorks is a cloud-based tool designed to simplify academic research and boost collaboration. Part of the Ex Libris suite, it provides unlimited storage for references and PDFs, making it ideal for large-scale projects and research teams.

It integrates with major academic databases like Google Scholar and PubMed. The Write-N-Cite plugin works directly with Microsoft Word and Google Docs, allowing users to insert citations and create bibliographies without leaving their writing environment.

Feature Details
Storage Unlimited for references and PDFs
Integration Google Scholar, PubMed, Word, Docs
Citation Styles Over 9,000 supported styles
Mobile Access Apps available for iOS and Android
Collaboration Real-time sharing and folders

RefWorks also includes tools for annotating, tagging, and organizing PDFs, all synced in real time. Its system of nested folders and multiple tagging options makes managing complex research projects easier.

With ProQuest Flow technology, teams can stay synchronized across devices, ensuring consistency and organization in shared projects. For individual users, institutional access unlocks premium features at no extra cost, such as:

  • Advanced citation detection
  • Unlimited cloud storage
  • Priority technical support
  • Integration with ProQuest databases

Data is stored securely with encryption, protecting sensitive research. The platform's drag-and-drop interface and automated citation formatting make it user-friendly, even for beginners. Plus, transitioning from other reference managers is seamless, with an easy import process that retains libraries and annotations.

While RefWorks is a strong choice for cloud-based collaboration, other tools like Sourcely are pushing boundaries with AI-driven features.

10. Sourcely: AI-Powered Academic Research

Sourcely

Sourcely takes academic research to the next level by using AI to automate time-consuming tasks, offering a streamlined experience for researchers. One of its standout features is the ability to analyze essays and suggest relevant academic sources automatically.

The platform simplifies PDF management with AI that extracts and organizes metadata for you. Its smart search function scans multiple academic databases, giving researchers broad access to scholarly content.

Feature What It Does
AI Analysis Analyzes essays and suggests sources
Integration Works with Google Docs and Microsoft Word
PDF Management Extracts and organizes metadata automatically
Collaboration Real-time shared libraries and co-authoring tools
Security Encryption ensures secure data handling

Sourcely also makes teamwork easier. Research teams can collaborate on shared libraries, annotate PDFs, and sync notes across devices in real-time - all while keeping version control intact.

The platform offers both free and premium plans, along with enterprise options for institutions. With encryption protecting sensitive data, it’s a reliable choice for handling confidential academic materials. Its integration with popular tools like Google Docs and Microsoft Word ensures smooth citation management, automatically formatting references in line with academic standards.

Switching to Sourcely is simple, too. The AI preserves annotations and metadata when importing libraries from other tools. The user-friendly interface combines advanced AI with straightforward navigation. Although it's a newer player in the reference management field, Sourcely tackles common research pain points like citation accuracy and information overload.

Comparison Table of Mendeley Alternatives

This table provides an overview of the latest features and pricing (as of January 2025), focusing on how these tools address Mendeley's limitations and cater to different research needs.

Feature/Tool Paperpile Zotero EndNote Sourcely ReadCube Papers
Base Price $2.99/month Free Custom pricing Free tier $15/month
Storage Unlimited 300MB free Based on plan Unlimited (paid) 10GB
Word Integration
Google Docs Native Via plugin Limited Native Via plugin
Mobile App iOS/Android iOS/Android iOS only iOS/Android iOS/Android
AI Features Basic No Limited Advanced Basic
Best For Cloud users Students Research pros AI enthusiasts Publishers

Feature Breakdown: Free vs. Paid Tools

Advanced Features Free Tools Paid Solutions
Citation Styles Zotero (9,000+) EndNote (11,000+)
Collaboration Basic sharing Real-time editing
PDF Management Manual sorting AI-powered tools
Data Security Standard encryption Advanced protection
API Access Limited Full access

A survey conducted in 2024 found that 59% of Paperpile users had switched from Mendeley, with better Google Docs integration and unlimited storage being the most common reasons [3]. Paperpile and Sourcely stand out for collaboration features, while Zotero remains the top free choice.

Pricing for Teams and Enterprises

Plan Type Small Teams Enterprise
Zotero Free Custom
EndNote $249/user/year Volume licensing
Paperpile $2.99/user/month Custom
Sourcely $6.67/user/month Custom

"The shift towards cloud-based reference management has been dramatic. Our data shows that 73% of academic institutions now prefer solutions with strong collaborative features and AI integration", according to a recent academic technology survey [3].

Most platforms now offer migration tools to help transfer libraries and annotations when switching services. Your final choice should align with your research goals, budget, and collaboration needs.

Conclusion

These tools not only address the gaps left by Mendeley but also bring features designed to meet the demands of modern academic work. Different tools cater to various needs across the academic community.

Zotero is a great option for students and early-career researchers, providing powerful features for free. For professional researchers, EndNote offers advanced capabilities, while Paperpile stands out for its smooth integration with Google Docs and generous storage options.

If you're working in a team, Sourcely impresses with its AI-driven tools, and ReadCube is a solid choice for its publisher-focused features. Each platform has its own strengths, making it easier to find one that fits your research style.

When choosing the right tool, think about these factors:

  • Compatibility with your word processor and research databases
  • Library size versus available storage
  • Collaboration tools for team projects
  • Budget and the features you need

Most platforms now offer migration tools, simplifying the switch from Mendeley. This makes it a great time to explore alternatives that better suit your workflow and research preferences.

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