Comparison

EndNote vs MarginNote 3

Price, ratings, monetisation and update history for both apps, side by side — with what reviewers say about each.

Head to head
About

EndNote

Manage your research from anywhere with this popular tool. Organize, search, and share academic papers and bibliographies seamlessly across devices. Sync your library and annotate PDFs on the go.

Highlights
  • Sync research library across devices
  • Search academic databases
  • Annotate PDFs
  • Import reference file formats
  • Share references with collaborators
  • Attach files from cloud storage
Features
Read full description

Collect, collaborate, create from anywhere with the EndNote app - the world's most popular research management tool. With flexible tools for searching, organizing, sharing research, and creating bibliographies, the EndNote app extends your ability to stay on top of cutting edge research and connect with your EndNote library on the go. EndNote enables you to easily view, edit, organize, and share research material on your iOS device. By syncing your research library across iOS, online, and desktop, you increase the power of EndNote by gaining seamless access to your reference library from multiple devices and platforms. The EndNote app includes: - Sign up for a free, EndNote online account or sign in to an existing account - Synchronize your library references, attachments, and PDF annotations to your online account and EndNote desktop - Built in web browser to search Clarivate Analytics Web of Science, PubMed, Google Scholar, your library catalog, or any other database you choose - Built in PDF viewer with wide range of annotation features. Annotations made can be synced and edited online and on the EndNote desktop - Importing capabilities for .ris, .nbib, and other popular reference file formats - Email and copy options for sharing references and file attachments with collaborators - EndNote “temporary citation” format support - Attach files from Dropbox, OneDrive or Google Drive to your references (accounts available separately) - Viewing and editing options for references and file attachments - Sorting, searching, and grouping options for references and file attachments - Getting Started Guide documentation

About

MarginNote 3

This app redefines studying by integrating e-reading with powerful annotation, mind mapping, and flashcard tools. Organize knowledge, connect ideas with hashtags, and enhance memory retention through spaced repetition. It offers a seamless workflow across multiple documents and devices.

Highlights
  • Integrated PDF/EPUB reader
  • Advanced annotation tools
  • Mind mapping and outline organization
  • Flashcard creation and Anki export
  • Multi-document support
  • Handwriting and Apple Pencil support
  • OCR for scanned PDFs
Features
Read full description

MarginNote 3, all brand new e-reader to better study and digest your books Integrating powerful tools for book annotation, mindmapping, flashcards and more, to build up your reading notes as never before. ============================================ Welcome to MarginNote. This is a highly powerful reading and study software and is applicable to Mac, iPad, and iPhone. By integrating the PDF/EPUB reader and multiple powerful study tools, MarginNote will enable learners to reorganize and connect knowledge from different aspects, then memorize and grasp it accordingly. Whatever your profession, such as student, educator, researcher, lawyer, or life-long learner, you may annotate and take notes through MarginNote, organize notes via Mindmap and Outline, connect knowledge horizontally via Hashtag and raise memory effect via the Flashcards. You will discover what MarginNote does is not to simply integrate these tools. Instead, it combines them deeply and skillfully, which makes it easier for users to toggle between different tools. What's New in MarginNote 3 * New and Clean UI Completely redesigned. * Improved performance and Running more smoothly * Support both Document Reading mode & Study Reading mode. * Excerpts & Note-taking * Enhanced Handwriting & apple-pencil support. * Support TextBox on PDF. * Support direct text-typing & sketching when editing note cards. * Support Auto OCR when excerpting on scanned PDFs. * Emphasis & Cloze * Support direct emphasis in powerful Emphasis mode both on PDF or Outline. * Support auto convert emphasis to Cloze in CardDeck. * Support creating Image-Occlusion flashcards. * Multi-Documents * Support both document tabs & split views to switch between documents. * MindMap * Auto grouping new excerpts by Document Table of Contents. * Support new brach display mode: Framework. * Swipe/Drag gestures to slide in/out Outline & Documents in Study mode. * Enhanced grouped cut/paste, drag to merge,.. etc. * Outline * Improved search and displaying keywords in results. * Improved styles. * CardDeck: * View Flashcards in MindMap mode and Document mode. * Enhanced Anki Export: Card styles, Image occlusions, Cloze * Enhanced Research web browser. * iCloud Sync * Fixed several design issue in previous versions. * More stable & improved performance. * Categories * Separate categories for Document, Study and Review. * Trash * Recover data from Trash and make data more safe. * Trial * 14-days free trial. MarginNote 2 features: Reading: - Support PDF and EPUB format; Annotating and NoteTaking: - Support text highlight and rectangular highlight; - Add notes directly at the page margin; the note editing area will not overlap with the book content at all; - Text, voice, picture, sketching and many other forms of comments in note; - Add hashtags to notes to facilitate the connection of notes; Outline and Mindmap: - Outline and Mindmap in one view; - Create Outline tree by swipe gestures; - Multi-selection editing such as group, merge, clone, etc; - Quick searching and filtering according to colors, hashtags, books. Flashcard: - Highlights and notes can be automatically turned into flashcards for review; - Spaced repetition adopting the Anki-based algorithm; - Switch to the linking book page at any time; iPad Pro & Apple pencil: - Split View of multiple tasks; - High-precision drawing by Apple pencil; - Fine tuned for Apple pencil; - Keyboard shortcuts; Import, Export and Sync: - Import webpages and notes from Evernote; - Export flashcards to Anki; - Export Outline to OmniOutliner; - Export Mindmap to iThoughts or MindManager; - Export to Evernote; - Export all the margin notes, MindManager, Outline and Pages to a printable PDF; - Sync books & notes with iCloud; Terms of Use: https://www.marginnote.com/press/marginnote-3-term-of-use Privacy Policy: https://www.iubenda.com/privacy-policy/92678020

Screenshots

EndNote4 screens
MarginNote 34 screens

Verdict

The call

The clearest difference is review sentiment: MarginNote 3 at 75% against EndNote's 28%. MarginNote 3 also leads on rating (4.7 vs 2.6) and ratings volume (5K vs 165). EndNote's advantage is in-app purchases (none vs 5). On price, ads, monetization model and device support there is nothing between them.

Scored on Price · Rating · Positive reviews · Number of ratings · Update frequency · Ads · In-app purchases · Monetization · Best chart rank · Devices · Requires iOS

CostPrice · In-app purchases · Ads · Monetization

Both are free to download. MarginNote 3 sells 5 in-app purchases, starting at $0.99 per month. EndNote asks for nothing beyond the download.

ReceptionRating · Positive reviews · Number of ratings

MarginNote 3 holds the better App Store score, 4.7 against 2.6. That said, the two scores are not equally well evidenced: MarginNote 3 has 5K ratings behind it against 165, so its average is the more settled of the two. Written reviews point the same way: 28% of EndNote's written reviews are positive against 75% of MarginNote 3's.

UpkeepUpdate frequency

EndNote ships an update every 4 months, MarginNote 3 every 6 weeks. The most recent releases landed on September 22, 2026 and September 23, 2026 respectively.

Scorecard6 real differences · 4 level
EndNote versus MarginNote 3: the parameters behind the verdict, then further details
ParameterEndNoteMarginNote 3
PriceFreeFree
Rating2.6 (165 ratings)4.7 (5K ratings) — better
Positive reviews27.6% of reviews74.6% of reviews — better
Number of ratings1655K — better
Update frequencyEvery 4 monthsEvery 6 weeks — better
AdsNoNo
In-app purchasesNo — betterYes
MonetizationFree with in-app purchasesFree with in-app purchases
DevicesiPhone, iPad, iPodiPhone, iPad, iPod
Requires iOS15.011.2 — better
Further details — not scored
Size91 MB392 MB
Age rating17+17+
DeveloperClarivate Analytics (US) LLCBeijing Yunsi Software Technology Co., Ltd

Customer experience

EndNote

All ratings165 ratings
Positive32.7%
Neutral14.5%
Negative52.7%
Written reviews369 reviews
Positive27.6%
Neutral11.9%
Negative60.4%

MarginNote 3

All ratings5,043 ratings
Positive93.2%
Neutral2.6%
Negative4.2%
Written reviews983 reviews
Positive74.6%
Neutral11.5%
Negative13.9%

User reviews

EndNote

From 165 App Store ratings

What we love

  • 🚀 Syncs well with desktop version
  • 📚 Convenient for reading and annotating papers
  • 💻 Good companion to desktop app
  • 🔍 Useful for managing references on the go
  • 🖋️ Annotation tools work well with Apple Pencil

Room to improve

  • 🐛 Crashes frequently
  • 🔍 Clunky search and organization
  • 📁 Sync issues and lost annotations
  • 🔒 Incompatible with other cloud storage
  • 🔧 Missing key features from desktop version

MarginNote 3

From 5K App Store ratings

What we love

  • 🚀 Powerful and efficient for studying and research
  • 👍 Excellent mind mapping and note-taking features
  • 💡 Unique and innovative functionality like video annotation
  • 🚀 Handles large volumes of documents and notes well
  • 👍 Useful for organizing and synthesizing information from multiple sources

Room to improve

  • 🐛 Frequent crashes and stability issues
  • 👎 Steep learning curve and lack of comprehensive documentation
  • 👎 Unreliable cloud syncing between devices
  • 👎 Cluttered and unintuitive user interface in some areas
  • 🐛 Bugs and glitches with certain features like handwriting and OCR

Bugs and requests

EndNote

Reported bugs

5 issues
  • Crashes when editing references
  • Indexing issues and lost library data
  • Compatibility problems with iOS updates
  • PDF viewer issues (e.g. no rotation, lost page position)
  • Login and authentication problems

Requested features

5 requests
  • Cite while you write functionality
  • Better PDF annotation tools (e.g. eraser, text notes)
  • Support for group sets and nested folders
  • Automatic citation data population from PDFs
  • Improved syncing and offline access

MarginNote 3

Reported bugs

5 issues
  • Syncing issues causing data loss across devices
  • Crashes and freezes when working with large documents
  • Inconsistent behavior with highlighting, erasing, and text formatting
  • OCR not functioning reliably for non-Latin scripts
  • Difficulty managing and organizing large document libraries

Requested features

5 requests
  • Improved export options and ability to share projects
  • Better integration with other productivity apps like Anki
  • More customization options for mind maps and annotations
  • Smoother handwriting experience and better palm rejection
  • Support for more file formats like PowerPoint

In-app purchases

None

EndNote

No in-app purchases

5 purchases

MarginNote 3

Subscriptions2
  • OCR Pro (Monthly)3 Days trial$0.991 Month
  • OCR Pro (Annually)3 Days trial$9.491 Year
One-time3
  • 14 days Free TrialFree
  • Unlock Full$12.99
  • Upgrade to Full$12.99

Questions

Is EndNote free?
EndNote is free to download, with no in-app purchases.
Is MarginNote 3 free?
MarginNote 3 is free to download, with in-app purchases available.
Which has better reviews, EndNote or MarginNote 3?
MarginNote 3 is rated higher. EndNote averages 2.6 out of 5 from 165 ratings, while MarginNote 3 averages 4.7 from 5K ratings.
Do EndNote or MarginNote 3 have ads?
Neither EndNote nor MarginNote 3 shows ads.
Which is updated more often, EndNote or MarginNote 3?
EndNote ships an update every 4 months, and MarginNote 3 every 6 weeks. Most recently, EndNote was updated on September 22, 2026 and MarginNote 3 on September 23, 2026.

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