Question 1

Is the new Zotero iPad app better than GoodNotes for PhD note-taking?

Accepted Answer

For my PhD workflow, Zotero has become better for the specific job of annotating papers because it keeps my notes directly attached to the reference. GoodNotes is still more sophisticated when it comes to pure annotation features, so it’s not a total “Zotero wins forever” situation. But for academic reading and keeping things organised, I’ve stopped using GoodNotes completely.

Question 2

How do you take notes on journal articles as a PhD student?

Accepted Answer

I download and organise my references in Zotero (on desktop and iPad), then I annotate the PDFs directly on my iPad inside Zotero. The key for me is that the notes stay with the paper, so I’m not juggling separate apps and losing context. After that, I sync my annotations into Notion so my reading actually feeds into my writing.

Question 3

Can you annotate PDFs in Zotero on iPad?

Accepted Answer

Yes—this is the whole reason my workflow changed. I’m LOVING the new annotation features in Zotero on iPad because I can read and mark up papers without leaving my reference manager. It’s not as feature-rich as GoodNotes yet, but it’s more than good enough for how I work day-to-day.

Question 4

How do you sync Zotero highlights and notes to Notion?

Accepted Answer

In the video I show how I’m syncing my Zotero annotations into my Notion system so everything ends up neatly in one place. The whole point is reducing friction—if I have to manually copy notes every time, I just won’t do it consistently. Once it’s synced, my Notion becomes the “thinking space” built from what I’ve annotated in Zotero.

Question 5

Do you still use GoodNotes as a PhD student?

Accepted Answer

Not for my PhD note-taking anymore. Since I can annotate within Zotero and keep my notes connected to my references, GoodNotes has become unnecessary for academic work in my setup. I still like it for personal journalling activities though.

Question 6

What is your PhD note-taking workflow with Zotero and Notion?

Accepted Answer

I bring papers into Zotero, read and annotate them on my iPad, and then sync those annotations into Notion. Zotero is doing the reference-manager job (and now the PDF markup job), while Notion is where I organise and build on the ideas. It’s simple, but it’s the first time my system has felt genuinely coherent.

Question 7

Is Zotero a note-taking app now?

Accepted Answer

Traditionally, no—Zotero is a reference manager, and GoodNotes is a note-taking app. But with the new iPad annotation features, Zotero is now covering a big chunk of the note-taking I actually need for reading papers. I do think it’ll take a while before it’s as sophisticated as GoodNotes for annotation, but it’s already changed how I work.

How I Take Notes As A PhD Student | Is the new Zotero app for iPad better than Goodnotes?

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