Comparison

Zotero vs MarginNote 5

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

Head to head
About

Zotero

This research tool helps you collect, organize, annotate, cite, and share your academic and professional work. Save articles, books, and webpages, add notes and highlights, and generate bibliographies in thousands of styles. Collaborate with others and sync your library across devices.

Highlights
  • Collect research from various sources
  • Organize with collections and tags
  • Annotate PDFs and webpages
  • Generate citations and bibliographies
  • Collaborate in group libraries
  • Sync across devices
Features
Read full description

Zotero is a free, easy-to-use research tool that helps you collect, organize, annotate, cite, and share your work. COLLECT • Save journal articles, newspaper articles, books, webpages, and more via the Share button in Safari and other apps • Automatically download article PDFs to read • Quickly add physical books and articles to your Zotero library by scanning book barcodes or article DOIs with your iPhone or iPad camera ORGANIZE • Use collections and tags to organize your research • View and edit bibliographic information for your research items ANNOTATE • Read PDFs, EPUBs, and webpage snapshots and add highlights and notes, or use an Apple Pencil to make freehand annotations CITE • Instantly generate citations and bibliographies in over 10,000 formats and journal styles including APA, Chicago, IEEE, MLA, Turabian, and Vancouver SHARE • Collaboratively collect sources and mark up PDFs in group libraries with your colleagues • Synchronize your personal and group research libraries to access them via Zotero’s desktop app and the Zotero website • Use the Zotero desktop app to insert your annotations into Word, LibreOffice, and Google Docs documents and automatically generate bibliographies from the sources you used Visit zotero.org to learn more about everything you can do with Zotero. Having trouble? Have an idea? Post bug reports and feature requests to the Zotero Forums at forums.zotero.org to talk directly to Zotero developers. ZOTERO AND PRIVACY Since 2006, the Zotero team has been committed to creating the best research software, and we believe that includes putting you in full control of your own work. We’re an independent, nonprofit organization, and we’ll never sell your data.

About

MarginNote 5

This app helps you deeply engage with reading materials by linking highlights to mind maps and flashcards for review. It offers task-based templates for various study needs, including question practice and vocabulary building, with AI assistance for tasks like creating outlines and extracting questions. Syncing and organization features ensure your study data is secure and accessible.

Highlights
  • Task-based reading templates
  • AI-powered question extraction
  • Mind map and flashcard integration
  • Offline dictionary for vocabulary
  • Secure sync with sync center
  • PDF and EPUB import
  • Handwriting and annotation tools
Features
Read full description

MarginNote is a PDF tool for in-depth reading and study. Keep PDF highlights linked to mind-map cards, then add those cards to review. MarginNote 5 introduces task-based templates for reading, question practice, and vocabulary. MarginNote has evolved since 2013. The upgrade from MarginNote 4 is free. Your study sets, notes, and purchases remain intact. MARGINNOTE 5: ONE TASK, ONE SETUP • Templates — a template sets the bottom tools, menus, pens, and excerpt colors. The "Standard" template has four modes: Excerpt, Handwrite, Organize, and Recall. Each mode groups tools for that task. • Template Gallery — install official templates in one tap. Some templates include examples to help you get started: – Card Practice: write answers by hand on question cards, check your answers, and focus your next review on questions you haven't mastered yet. AI can split a whole workbook into cards. – Reading Vocabulary: collect words while reading English; an offline dictionary provides base forms, pronunciation, and definitions, and finished cards join review when automatic review is enabled. • Make it yours — the corresponding controls are highlighted as you edit. Find features and settings with Feature Search, and export or share your templates. • Traditional Interface — open the template menu and choose "Traditional Interface" (except on iPhone Duo). SYNC YOU CAN SEE The home screen shows where sync stands. The Sync Center lists notes and original documents separately and tells you when a document is still downloading. Manual sync reports results and offers a protective snapshot. Applying cloud changes also protects local study data. THE CARD AT THE CENTER • Organize excerpts by chapter; for books without a table of contents, AI can build one. • Title Links — notes on concepts you've studied resurface as you read new documents. • Extend — open writing space anywhere on a PDF: inline, in the margin, or folded away. AI AS AN ASSISTANT, NOT A SUBSTITUTE AI Breakdown · Question Extraction · AI TOC · AI OCR card templates · translation · chat. Save any answer as a card, or turn its outline into mind-map branches. Online AI sends task text or images to the service provider used for the request. REVIEW: THINK FIRST, THEN LOOK Use Recall mode to hide and reveal answers in the mind map. Add cards to a review deck for FSRS spaced repetition. Write directly on card snapshots while you review. On iOS/iPadOS/macOS 26+, when Apple Intelligence is enabled and its model is available on a supported device and in a supported region, on-device recall hints work offline without MarginNote credits. THE FULL WORKFLOW PDF, EPUB, Office-to-PDF import (online), video and audio · Zotero, cloud drives and external folders · side-by-side documents · handwriting layers and mind-map backgrounds · mind-map PDF export (structure or card flow) · read aloud · fast OCR WHO IT IS FOR Anyone who rereads material and needs to remember it: medical and law students, exam takers, researchers, language learners, serious readers. ACROSS YOUR DEVICES iPhone, iPad and Mac with one Apple Account; iCloud syncs study sets, notes and review progress. Native Apple Pencil handwriting on iPad. Also adapted for iPhone Duo. ABOUT PURCHASES Free to download. Some features require Pro (one-time unlock) or Max (subscription or one-time unlock). MarginNote Agent requires Max and uses MarginNote credits. Some online AI uses MarginNote credits; external AI is billed by its provider. A Max subscription includes 500 credits/month while active. Questions: service@marginnote.com Terms of Use: https://dist.marginnote.cn/MarginNote_Terms_and_Conditions.pdf Privacy Policy: https://dist.marginnote.cn/MarginNote_Privacy_Policy.pdf

Screenshots

Zotero2 screens
MarginNote 54 screens

Verdict

The call

The clearest difference is in-app purchases: Zotero at none against MarginNote 5's 10. Zotero also leads on review sentiment (78% vs 58%). On price, rating, ratings volume and update cadence 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 5 sells 9 in-app purchases, starting at $4.99 per 3 months. Zotero asks for nothing beyond the download.

ReceptionRating · Positive reviews · Number of ratings

On the App Store both sit at effectively the same score — 4.6 for Zotero against 4.5 for MarginNote 5. Both are backed by a comparable volume of ratings — 436 and 741 respectively. Written reviews are what separate them: 78% of Zotero's written reviews are positive against 58% of MarginNote 5's.

UpkeepUpdate frequency

Both ship on a similar rhythm, roughly every 3 weeks. The most recent releases landed on November 7, 2026 and November 11, 2026 respectively.

Scorecard3 real differences · 7 level
Zotero versus MarginNote 5: the parameters behind the verdict, then further details
ParameterZoteroMarginNote 5
PriceFreeFree
Rating4.6 (436 ratings) — better4.5 (741 ratings)
Positive reviews77.9% of reviews — better58.5% of reviews
Number of ratings436741 — better
Update frequencyEvery 3 weeksEvery 3 weeks
AdsNoNo
In-app purchasesNo — betterYes
MonetizationFree — betterFree with in-app purchases
DevicesiPhone, iPadiPhone, iPad, Mac — better
Requires iOS16.6 — better17.0
Further details — not scored
Size237 MB372 MB
Age rating4+4+
DeveloperZoteroBeijing Yunsi Software Technology Co., Ltd

Customer experience

Zotero

All ratings431 ratings
Positive89.6%
Neutral4.9%
Negative5.6%
Written reviews263 reviews
Positive77.9%
Neutral10.3%
Negative11.8%

MarginNote 5

All ratings741 ratings
Positive86.4%
Neutral3.4%
Negative10.3%
Written reviews568 reviews
Positive58.5%
Neutral15.5%
Negative26.1%

User reviews

Zotero

From 436 App Store ratings

What we love

  • 👍 Simple and powerful
  • 🚀 Convenient and useful
  • 🚀 Seamless syncing across devices
  • 🚀 Excellent reference management
  • 👍 Great annotation and PDF reading experience

Room to improve

  • 🐛 Crashes frequently
  • 🐛 Syncing issues with WebDAV
  • 🐛 Metadata not automatically extracted from PDFs
  • 🐛 Annotation tools could be improved
  • 🐛 Limited sorting and filtering options

MarginNote 5

From 741 App Store ratings

What we love

  • 🚀 Powerful features
  • 📚 Great for academic/research use
  • 👍 Useful note-taking and organization
  • 🖊️ Improved handwriting and annotation

Room to improve

  • 🐛 Buggy and crashes frequently
  • 🕰️ Slow and laggy sync between devices
  • 🤯 Steep learning curve, poor documentation
  • 💰 Expensive upgrade from previous version

Bugs and requests

Zotero

Reported bugs

4 issues
  • Unable to unzip PDF snapshots
  • Annotations disappearing or moving unexpectedly
  • Dark mode not working as expected
  • Inability to add citations directly from the app

Requested features

6 requests
  • Eraser tool for annotations
  • More color options for pen and highlighter
  • Ability to open PDFs in external apps
  • Bookmarking and table of contents support
  • Improved search functionality
Show 1 more
  • Offline access to downloaded PDFs

MarginNote 5

Reported bugs

3 issues
  • Disappearing annotations when using extend function
  • Inability to restore accidentally deleted mind maps
  • Inconsistent behavior with PDF file management

Requested features

4 requests
  • Improved iCloud/cloud sync reliability
  • More intuitive and user-friendly interface
  • Better support for external document libraries
  • Ability to disable auto-excerpt selection

In-app purchases

None

Zotero

No in-app purchases

9 purchases

MarginNote 5

Subscriptions3
  • Subscription to MAX (3 months)7 Days trial$4.993 Months
  • Subscription to MAX (Annually)1 Month trial$12.991 Year
  • MarginNote Max Annual1 Month trial$16.991 Year
One-time6
  • 14 days Free Trial2 variantsFree
  • Upgrade to PRO from MN3(iOS)$4.99
  • Unlock PRO Forever (New)$12.99
Show 3 more
  • Upgrade to MAX from MN3(macOS)$19.99
  • Unlock MAX based on PRO (New)$40.00
  • Unlock MAX Forever (New)$51.99

Questions

Is Zotero free?
Zotero is free to download, with no in-app purchases.
Is MarginNote 5 free?
MarginNote 5 is free to download, with in-app purchases available.
Which has better reviews, Zotero or MarginNote 5?
Zotero is rated higher. Zotero averages 4.6 out of 5 from 436 ratings, while MarginNote 5 averages 4.5 from 741 ratings.
Do Zotero or MarginNote 5 have ads?
Neither Zotero nor MarginNote 5 shows ads.
Which is updated more often, Zotero or MarginNote 5?
Zotero ships an update every 3 weeks, and MarginNote 5 every 3 weeks. Most recently, Zotero was updated on November 7, 2026 and MarginNote 5 on November 11, 2026.

Other comparisons