How do you use Obsidian?

Hi MPUers, I just started using Obsidian after listening to the MPU’s Obsidian episode and hearing it from y’all here. I am, however, trying to figure out how to use it? I am a bear user and trying to figure out how to set up my workflow.

  • Can you share how do you use Obsidian?
  • What do you store/organize notes in it and how do you organize attachments?
  • Automations you have set up?
  • What plugins do you use?
  • Themes?


PS: Posting it here since I felt a little overwhelmed at the Obsidian community and felt at home here. Also, we all kinda use similar tools and are automation nerds!


I started using Obsidian, making several vaults (collections of notes and files), organized around different areas of interest. This proved to be too complex, since linking between vaults is not simple – in fact it is annoying. So, I’ve consolidated into two vaults, one for most of my writing and note taking, another that will not explain publicly.

Anyway, I always prefer folder hierarchies, so that’s how I arrange my “writing” vault internally: by categories and topics within categories. I also use daily notes as a kind of “hub” and collector for small observations and diary-type notes. Since I do not like to have all daily notes in one big tub, I’ve configured my daily note “Date Format” within the Daily Notes plugin settings as


This has the clever result of causing Obsidian to automatically create folders for Years, then Months within Years and then my dailies for the month. The daily notes are named like this: 2021-09-03 Fri.

I configured Obsidian to put all attachments in an Attachments folder at the root. If I drag a PDF or an image or a video into a note, the file is place by Obsidian into Attachments and a link to it in the note. I keep attachments in the Attachments bucket because there’s no point in distinguishing among them – If I really need to do that for some reason (which hasn’t happened yet), I would open that folder in Finder and sort it there.

I don’t know what the OP means by “Automations you have set up”. Obsidian does many many things by configuring plugin settings – what I do would not matter to anyone else. So I’ll skip that question.

I don’t use Zettelkasten. I’ve learned that most things I think about are not worth remembering – ZK’s obsessiveness seems to foster poor rationality.

I use the Minimal theme, dark mode, configured with the “Minimal Them Settings” plugin, and a hierarchy of CSS snippets stored in the .obsidian/snippets folder that control colors and other tweaky things the way I like them.

I use a ton of plugins.

Two favorite plugs are Readwise Official with custom formatting of Readwise notes synced by the plugin, controlled on the Readwise site. And Footlinks. Footlinks neatly solves the problem of having really long URLs visible in the body of a note in edit mode. Footlinks grabs these links and makes them footnotes at the end of the document – makes for a very clean “almost WYSIWYG” editing experience.

I also use the official Publish and Sync plugins.

Everyone should grab and learn to use the Dataview plugin. It brings notes alive. One of the sections of my main vaults is a log of technical changes I make to my computers – configurations, problem solutions, etc. – I use Dataview to create summary notes that index these logs. It’s like a personal customized technical knowledge base focused on the hardware and software I use.

BTW, if you like to make notes when you’re out and about, and clip pictures of documents or whatever to the notes, Obsidian on an iPhone, with a vault synced to the desktop, is wonderful. Obisidan integrates as well with the camera as does Agenda or Bear – because iOS. No magic here, just fun.

I also index big chunks of my vaults to DEVONthink, because sometimes DEVONthink is better for some tasks. I don’t use DEVONthink to Go with Obisidan, or for much else for that matter.

My advice: walk very very slowly. Don’t run or copy what other people do unless it makes absolutely perfect sense to you. I’ve used Obsidian since literally the first minute it was made public. I’ve torn apart and rebuilt vaults many times to get to the point I am comfortable with what I have. THERE IS NO RIGHT WAY – don’t let anyone tell you there is.


… Also – subscribe to Eleanor Konick’s Obsidian Roundup. She is an Obsidian forum moderator and publishes a weekly newsletter summarizing the best of that week’s discussions, plugin updates, etc., from both Obsidian forums. Also, she has really great thoughts about note taking, digital gardening, and other facets of using software. All this for $1/month.


I use Obsidian for notes that I make about research. Mostly reading academic papers and linking concepts between the notes. I have index notes (sometimes billed as maps of content) with links to notes that are related. For me, that’s a lot of brain areas, Parietal Lobe is the index for Superior Parietal Lobule, Inferior Parietal Lobule, etc.
I use the Citations plugin to read a .bib file that is automatically updated by Zotero, my reference manager.
My highlights and notes from PDFs are exported as needed (by a Zotero plugin) into a References folder in Obsidian, so they are easy to link to in my notes.

I don’t put much else in Obsidian, no tasks, no daily notes, etc. I find that these ‘pollute’ the space. As I mentioned elsewhere, it’s like having a toilet in your living room - it saves steps, but the purpose of the living room becomes unclear. For tasks, daily notes, and project-related notes, I use NotePlan with very little linking between notes. For my ‘lab’ notes (procedures and notes about analyses), I use Notebooks since it runs on Mac, iOS, and Windows (unfortunately, not Linux).

So while a lot of people put all these things into Obsidian (perhaps using vaults, folders, or tags), and it works well for them, I find that having different contexts helps me know which notes/things are in the app I’m working on.

I also find that putting All of the Things™ into a single app often leaves me wishing for features to automatically do things or connect things, when in fact it is better for me to just do those things myself. This little bit of extra work has the desirable side-effect of helping me remember and retain information better. Easier isn’t always better.

Edit to add: Agree with @quorm above, develop your system, then find tools that will help you execute on that system. If a tool goes away, or goes to an expensive subscription, or the author is a twit, you still have your system.


I have a very similar system to you. I too find that I like to have separate spaces (with the same general plain text markdown logic) for different things. I’m a researcher and physician. My research notes on articles live in Zotero & Obsidian (using zotfile, zutilo, and mdnotes plugins). My plans live in Noteplan, and I do occasionally open that folder as a separate obsidian vault to use the Kanban plugin, which often gives me a better sense of the big picture of my projects & their associated notes.

My other category which might be similar to your lab notebook is notes about clinical medicine (useful figures, etc). I played with using a separate Obsidian vault for this but I’d initially started using Bear for this and find that I really like the experience, particularly on iOS where I feel like the speed of reference is slightly better than Obsidian. I think with time I may switch this over but like you I kind of like having different notes/contexts for different kinds of work.


Here is a concise overview of how I use Obsidian.

Two Vaults;

  • Work
  • Personal

Work Vault:

  • Meeting and project notes
  • Written communications and speaking notes
  • Reference material and non markdown files, e.g., PDFs, for important information.
  • I have created MOC notes for specific areas of work
  • I make heavy use of templates

Persona Vault:

  • Book text and material
  • Book and article research, lots of MOC notes and linking
  • Blog articles
  • Quick reference information
  • Readwise Official
  • Writing Archive (I converted decades of prior material to markdown and placed all of it this Obsidian vault

I do NOT use Obsidian for:

  • Managing projects or tasks
  • Calendar events
  • Mind mapping
  • Extensive document storage

I am a researcher and physician as well trying to learn how to use Obsidian for my research and reading. Would you be willing to share your workflow?

Sure, I’d be happy to! It’s always in flux but this is the general outline of it. The backbone of my system is plain text markdown notes, which as I mentioned above I keep in three major categories. I think you can do all of this in Obsidian – my use of Bear & Noteplan is mostly due to habit, preference, and the fact that I started this system before Obsidian was available on iOS. But the broad strokes are below:

For research, I get access to new papers through my RSS reader. I follow the major journals in my field and also some smaller ones in my sub-field of interest. I’d like to say I check this on a regular basis but honestly I tend to wade through those when I have time. That could be every week, once a month, less during busy work periods. Articles which I find interesting or potentially useful for research I’ll then put into my reference manager, Zotero. I have a loose categorization and tagging system there which is a work in progress, but generally use collections for either specific projects I’m working on or big categories of literature I’m sorting through, and I tag based on smaller themes (as well as whether I need to read it, revisit it, flesh out my notes, etc) and also have a project-based tag for each project, large or small, which is consistent across my zotero, task management, and obsidian systems. For naming and filing the associated PDFs, I use Zotfile to rename the files (pretty simple: Author Year - Title) and put them in my references folder in my cloud storage. After I import the reference and tag it, etc., I will also create a literature note for it in Obsidian using the MD notes plugin. Because I prefer to title my own notes, I’ve been using the standalone note function to name the mdnote file the same as the PDF.

In terms of actual notetaking, my Obsidian research vault contains:

  • a literature notes folder containing the notes created with mdnotes
  • a folder I call “synthetic notes”: this contains notes on particular concepts or themes, usually one or two words, that I build out as I read on particular topics. these notes are probably most similar to maps of content.
  • a folder of author notes: this folder contains notes for each significant scholar whose work I engage with – the notes are tagged based on the theme areas they work in & there’s a bibliography of their work that I update with links to my own literature notes and other resources about them. I also connect them with their co-authors or frequent collaborators, or with scholars whose work they are building on. these are always works in progress.
  • a folder I call notes & fragments: these are random jottings that I might take which don’t necessarily fit into any of these other categories. I often capture these on the fly when I’m out with just my phone. I recently started using Drafts to capture these but I’m tool agnostic on that front. these notes are named with the date and a few keywords.
  • a folder of project hubs: these are central notes for different writing projects I work on, with links to useful notes and resources, including the associated zotero collection, for each.

I do also use daily notes often in this vault, but they are less important here than in my task management system in Noteplan. Oh, and here are the plugins I use:

For actually writing manuscripts, for things I am working on alone, I write in markdown and convert the final product to Microsoft Word/PDF depending on where I’m sending it. For collaborative work I often find myself working in Google Docs or Word depending on the project.

For notes on clinical practice, I use markdown notes in Bear. Bear doesn’t have folders, which is helpful because I’ve always found it hard to categorize topics in medicine cleanly. For structure, I use tagging heavily and interlink the notes together. This aspect of my note taking is pretty straightforward – I might have a note about hypertension with general information, links to my notes about each anti-hypertensive med, a section on monitoring for complications with links to my notes about each of those, etc. I don’t think much about the structure of this since these are notes often taken on the fly. If someone is doing a chalk talk I might take a photo of their whiteboard, name the note and tag it, and plan to flesh it out later. It’s mostly just meant to be useful to me and easy to maintain.

My task management is pretty simple. I’ve found that I tend to think better with bulleted notes, etc, so I use Noteplan to plan out my projects, take meeting notes, and just write random meta-things about how I’m working. I use Apple Reminders with Goodtask to manage my tasks with hard deadlines (visible for me on my calendar using Fantastical) and for the rest I use Noteplan’s task management. I used to use Trello for a broad overview of my projects but switched to opening my Noteplan folder as an Obsidian vault during my weekly review in order to use the Kanban board. I’ve found that pretty fruitful!

Hope that was helpful, and happy to go more into the weeds on any area.


Very interesting.
Particularly the author notes, and opening the NotePlan folder in Obsidian.


I like your date format tip to create folders. I’ll need to check that out.

I’ve been keeping a daily work journal in Obsidian, which has been a life-saver because I’ve got so much going on between my business and volunteer work. If I have a meeting, I quickly add a section (line), a title, write some notes, a hyperlink to the project page, and then one or more tags. I’m not sure about the tags… I can’t say that I’ve found them to be overly helpful yet but I feel compelled.

Question: I’ve been wondering whether somehow splitting my day into several pages/ files, i.e. a meeting gets its own file, might somehow be more advantageous with searching and/or tag use. So far I’ve just been doing one file/ page per day with formatted sections.

Comment: I really like- love- being able to insert a hyperlink in my daily journal to a work project and then jotting a small note on that master page with a link back. It has made tracking things so much easier.

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