Picking a Markdown Editor That Works for Real Remote Note Chaos

Table of Contents

1. Why markdown structure matters when everything else breaks

I have four note apps open right now. One is frozen, one forgot my last edit, one synced something out of order, and the last one actually works — because it’s just a .md file in a folder synced with Syncthing. Markdown doesn’t solve everything, but it gives you portable structure when the app layer keeps letting you down.

It’s not just about plain text. The ability to define headers, bullet hierarchy, code blocks, and tables lets you build actual repeatable structure for planning and documentation — without depending on some proprietary format or internet connection. If you’ve ever overwritten a Notion database row mid-flight, you know why this is huge.

The most important thing I keep forgetting: the structure is useful only if I can get back into it fast. That means:

High performance on huge files (some of mine are 50k words+)
Keyboard-only navigation, predictable formatting toggles
Actual outline support or sidebars that follow heading structure
Frontmatter support that doesn’t crash the parser
Zero risk of data loss from autosave timing

It doesn’t matter how pretty the preview is if the sync delay loses your daily template again.

2. How Obsidian handles local vault chaos better than most

Obsidian’s core win isn’t the graph or the plugins — it’s how it keeps everything in a local folder as Markdown files first and foremost. Every time I break something in a plugin (and I do, weekly), my notes still render just fine in any other editor. That reversibility is gold.

Here’s the setup that works for me at the moment — but honestly might fall apart by next week:

Vault folder synced by Syncthing to other devices
Daily Notes plugin with a custom template (but remember: if you use {{date}} without checking plugin order, it just outputs the string)
Hotkeys for new note, link current highlight, toggle view — this bypasses most of the UI jank
Calendar plugin only works reliably if you disable backward date parsing after March — no idea why

Lately I ran into this issue where the backlinks panel stopped updating after note creation. Turns out it was a plugin conflict with Sliding Panes — disabling that fixed it instantly, but you’d never guess unless you dug into the logs. There’s no visible error. It just… silently stops working.

Still, Obsidian wins because even if it fails quietly, your content lives on your drive, structured, and portable, ready to open in VS Code or whatever fallback you bolt together in crisis mode.

3. The unexpected power of Zettlr for structured academic style notes

Zettlr
didn’t catch my eye at first — I skipped it a few times because the screenshots looked like another Electron app trying to be a text editor. And to be fair… it is. But the way it handles citations, Pandoc exports, and folder-level tag logic is ridiculously efficient if you’re managing large collections of research notes, source excerpts, or even blog drafts with metadata.

I set it up with a nested folder structure for reference-style notes, and the YAML frontmatter support finally let me separate note type from note title sanely. Exporting the whole thing to PDF or even DOCX using custom CSL styles actually worked on the first try — which is more than I can say for Notion’s garbage export fidelity.

One small bug I ran into: if you alt-tab too quickly after using the export dialog, Zettlr sometimes forgets the export path and defaults to the root directory. It doesn’t warn you. It just sends your PDF to a different folder than you expected. First time it happened, spent 20 minutes trying to re-export before realizing it already had — just buried somewhere else. Close the app and reopen, and it remembers the proper path again.

Zettlr is weirdly good at surfacing long forgotten headers from your archive. It uses simple fuzzy matching on filenames and H1s, but the relevance ordering mostly makes human sense. Not sure what they’re doing behind the scenes beyond just index caching, but it’s better than VS Code’s ctrl-p in a big vault.

4. Foiled by MacDown’s live preview and its silent rendering errors

MacDown’s got the best live side-by-side view for Markdown if you live in a single file at a time. It’s fast, pure, and perfect when you’re editing documentation meant to get shipped out in HTML anyway. But it has a silent failure mode that cost me a whole chunk of client notes once: if you write a fenced code block and forget to close it, the entire preview pane breaks… silently. It just stops rendering below that point. No warning. No red marks. Just blank.

I didn’t notice until hours later. Luckily the raw Markdown was fine, but the fact that the preview pretends everything’s okay up to the failure point made it way worse. Even now, whenever I open those files, I double check for triple backticks like a paranoid raccoon.

The bigger issue? MacDown doesn’t remember your open tabs unless you manually set that in system preferences under “Close windows when quitting an app”. And if macOS updates, sometimes that resets, and you lose your session. Not MacDown’s fault, but definitely not obvious when it happens.

If you’re doing local-only editing and don’t need backlinks, MacDown is still one of the cleanest tools. But only if you trust yourself not to forget a closing `.

5. Why Typora works until you try automating folders

Love Typora. Hate Typora. It’s beautiful and fast, and the clean WYSIWYG markdown makes it practically invisible while writing — which is great until you start needing repeatable structure or templating across dozens of files.

I tried to use Typora for rough-drafting daily notes. Files are named by date, each one has three H2s and a checklist block. I wrote a small shell script to generate them into my working folder, and suddenly, Typora couldn’t see the newest ones. Turns out it cached the folder content based on when you last opened it, and if the generated filename was too fresh (like within the last few seconds), it sometimes just didn’t show up until restart. Again: no error. Just incomplete file lists.

This is the kind of thing that you only catch if you’re watching your Finder window while running the script and comparing what shows up — and I was, because I thought my script was broken. Nope. Typora’s folder pane just hadn’t refreshed yet.

One weirdly cool thing about Typora, though: it handles embedded images better than most Markdown editors. Just drag and drop from clipboard, and it auto-saves to a relative path in a clean folder. None of the others do that without plugins or gymnastics.

6. VS Code delivers structure but leaves you building your own views

If you’re already living inside VS Code with Git integrations and custom keyboard maps, then yeah — Markdown editing there makes a weird amount of sense. The syntax highlighting is predictable, search is global, and with the right extensions, you can turn it into a structured knowledge base. But it’s on you to put the pieces together.

For example, I wanted a collapsible outline pane that pulled just H1, H2, and H3 from `.md` files in a specific folder. Total rabbit hole. I landed on a combo of the Markdown All in One extension and some Workspace-specific settings to filter files — but it still ignored anything in hidden folders by default. And no, this isn’t documented clearly anywhere.

The real catch: VS Code handles markdown links fine, but the click-to-jump behavior breaks hard if your filenames differ from your display titles. That’s an edge case that only hits if you’re mixing CamelCase and spaces. Once I cleaned up the underscores, the internal navigation started working again. Painful discovery, but the fix was obvious once I saw it happening in the devtools.

This stack is ideal if automation is part of your life. You can script, sync, and version control everything. But if you just wanted a note open in three seconds because someone just threw a Zoom link in chat? It’s a hard sell without muscle memory.

7. Table editors are missing or underbaked in almost every option

Tables in Markdown are a trap. All of these editors claim support — and yeah, technically rendering a table written like | header | row | works. But try editing one with more than four columns and mixed-length values? It starts breaking alignment, loses column width consistency, or mis-renders on preview.

Only a few options mitigate this well:

Obsidian has a plugin for Excel-style editing, but it only works on plain cells — nested MD inside cells trips it up
Typora has auto-alignment on Tab, but it breaks if the last row isn’t fully populated
VS Code with Markdown Table Formatter sort of works, but turns into column soup on long lines

The best workaround I’ve landed on is literally editing tables in Airtable, exporting CSV, running a script to convert to GFM MD table format, and pasting that in. I shouldn’t have to do this. But the reality is: no in-editor table features are reliable under actual messy data conditions.

Also: if you try to embed tables generated from scripts, Obsidian sometimes strips out the pipe alignment on save if you edited the file elsewhere. Huge edge case. Very annoying if you use external renderers like Hugo.