Best Note-Taking Tools for Entrepreneurs Who Juggle Chaos

Table of Contents

1. Notion works until your brain breaks its block logic

Notion is still my default daily stack because it lets me hurl half-formed ideas, client calls, screenshots, database references, and a dozen backlogged ideas into a semi-visible structure I can at least pretend to organize later. The problem kicks in once you start to trust it too much.

Here’s what happened: I set up a synced database for weekly strategy logs across several projects. Each entry had nested toggles, linked databases tracking deliverables, and embedded comments from a virtual assistant. It felt great—until I tried to re-filter a gallery view using a page property from another synced database. Nothing showed up. Nothing. It wasn’t broken. It was just doing something completely different than expected. Turns out, Notion only evaluates filters using the current page’s context when linking databases—even if it visibly offers cross-db filter options. What looked logically valid just silently failed.

Undocumented edge: Relational filters don’t always behave predictably inside linked databases when those links are duplicated across templates. Sometimes the relation input resets to the default template value even if you manually set the filter again.

Tip stash:

If you’re doing multi-project planning, avoid nesting template buttons that reference synced blocks. They now conflict on refresh.
Use status or select fields instead of booleans for shared progress views—checkboxes won’t filter cleanly across teams long-term.
Always verify each workspace has identical font/render settings. Looks minor, breaks PDF exports daily.
Toggle headers inside synced blocks often collapse randomly if another editor opens the page in a different browser.
Use the sidebar’s outline mode to eyeball chaos before it escalates into 30 pages of toggles.

2. Obsidian is incredible unless you expect normal app behavior

I love Obsidian because it gives me that raw control—markdown files, custom aliases, plugins with zero help text, and sidebars that feel like command-line panels. But I’ve rebuilt my setup from scratch four times because of sync issues no one warned me about.

I kept noticing subtle file drift: edits lost, titles mismatched, tag links that showed up in backlinks but 404’d on click. Eventually tracked it to how the Obsidian app writes to disk before fully loading all links in heavily crosslinked vaults. If you use iCloud Drive or even Dropbox, that initial async write process creates a minor but compounding edge case: the preview cache updates before the actual file structure syncs. Result? You’re linking to ghosts.

I had one vault where the file Strategy-Weekly-SEO.md looked fully editable, but all tags filtered wrong. Turned out the actual file was overwritten by a different machine that crashed before graceful close. Obsidian never prompted a conflict. It just assumed it was fine.

The aha moment was dumping the .obsidian settings folder and watching the hot mess resolve into sane-looking links again. That folder stores plugin config, hotkeys, and internal cache logic—but does not auto-heal if the vault gets corrupted remotely.

3. Tana flips your workflow logic and then asks you for money

Look, I want to like Tana. I keep trying. It feels like what Contexts in Roam should’ve been. You can zoom into any node, spawn tasks recursively, nest topics under roles, and it all still looks sleek… until you start rethinking your entire data hierarchy for the tenth time because one of your references isn’t showing under the supertag it’s technically tagged with.

Here’s the hiccup: Tags are nodes. Nodes are fields. Fields are objects embedded in pages. All of those can be queried, but not with one consistent syntax. Example: I had dozens of client calls tagged #ClientCall with a field Project = Campaign-X. Simple, right? But querying #ClientCall AND Project: Campaign-X returned an empty list unless I explicitly opened each node and waited for it to resolve the schema live on-screen. It only worked after I manually triggered focus for half the nodes. No visibility into why.

“The field exists, but at render time, the tag reference doesn’t bind because the compiled tree isn’t hydrated yet.”

Yes, that’s a sentence I had to write in support chat. The support person sympathized but confirmed it’s just… how Tana works for now.

4. Apple Notes is the fastest trapdoor to total forgetfulness

If speed is your only priority, Apple Notes wins. It’s fast enough to jot something mid-call while leaving the camera on and staying present. Typed text shows on all devices almost instantly. The problem is once you use it for anything systemic, it vanishes into a black hole of stale assumptions.

Case in point: I created weekly to-do lists in Apple Notes, each with nested checkboxes, a timestamp, and links to Notion documents. Week-over-week archiving by duplicating the previous note felt straightforward. Then I realized none of those links actually worked on my iPad. Apple Notes visually renders web links differently on iOS vs macOS—and often strips deep links if the link text was edited after pasting. Worse?

Flaw: When duplicating a note that includes checklist items, the completion status silently copies over—so half your “to-dos” look done until you tap one and it resets the cache.

It took me three weeks of missed subtasks to debug that behavior. No popups. No obvious reversion. Just fake progress.

5. Logseq made sense until I added calendar sync

Backlinking works beautifully in Logseq. Daily journal? Easy. Meeting notes that auto-reference a topic? Magical. Calendar sync? Instantly catastrophic.

What threw me was how Logseq rewrites synced calendar entries as markdown pages in your graph. That’s fine… until the same calendar entry updates. I had event titles like “Weekly Standup – AGENCY” get rewritten multiple times because I updated Google Calendar invites to clarify ambiguity. Each rename created a new node. Each new node retained historical backlinks—but now my graph had three nodes pointing to the same meeting with different audit notes attached.

There is no deduplication. No rename tracking. Once a calendar node is saved with a title, it lives forever—even if the original event changes. I eventually found a plugin that does fuzzy matching to stitch them together, but it had to be manually run. So now every week includes a 5-minute ritual of “merge orphaned events” before I can trust anything written in tags across each meeting.

6. Coda’s formulas are great until they start executing late

I use Coda when I need to build things that should’ve been Airtable apps but kept hitting limits. The formulas are powerful—until the delays start. Basic table formulas work instantly, no issue. But the moment you use a button to trigger a sequence that updates another row using RunActions(), you might start seeing what I did: a 2–4 second lag before anything appears to happen, if at all.

I built a lead scoring board where people reviewing cold emails could hit “Mark as Promising,” which triggered a vote counter and moved the row to a follow-up table. Everything tested fine except for one reviewer who messaged, “uh it ate the row.”

Turns out:

Delay was caused by another view refreshing in a hidden section. Yes. Hidden views still process state triggers.
Automations fired twice if the same row received two manual inputs in under ~500ms.
Using If(thisRow) inside a button formula sometimes evaluates differently depending on window size. Genuinely not kidding. Fullscreen caused a different render cascade.

Refactoring it to trigger an automation instead of using inline buttons fixed it, but made UI worse. Essentially a trade-off between clarity and timing.

7. Craft Docs feels like productivity theater until it’s not

Craft is gorgeous. You’ll never write a checklist that looks better. But… I used it for three weeks thinking it was superficial. Then I found templates and bi-directional backlinks. They’re less powerful than Obsidian, but way easier for teams that need prettier docs without teaching regex to interns.

One thing that tripped me: If you paste in content with internal hashtags like #events or #2024Q2 into Craft, it makes the visual tag—but unless the tag exists somewhere else in your workspace structurally, clicking it does nothing. It’s decorative. Not functional. I found out because I handed a doc to a collaborator and she said, “Where does this link?” It didn’t. It just scrolled the page back up.

The feature kind of half-works, depending on whether the tag has ever been clicked from a block view elsewhere. So you end up doing weird prep work like creating a blank page for each expected tag just to activate link behavior.

If it’s not in a navigation pane, it’s Schroedinger’s tag.