Finding the Perfect Self-Hosted Notes App: Setting Up the Experiment

Introduction

Today, you’re in for a treat: you get to see my process for setting up an experiment to find the right self-hosted note-taking app. If you’re someone who values simplicity, Markdown, and owning your data, this post is for you.

I’m a dedicated note-taker. Every day, I log my work, jot down highlights, create fleeting notes for random ideas, and capture meeting details. I also take notes while reading books or articles, recording anything that resonates with me.

For a while, Obsidian has been my go-to tool, but lately, it feels like it’s become too much. The endless plugins, extensions, and customizations—while powerful—overwhelm my desire for simplicity. Yes, I could strip Obsidian back to its essentials, but truthfully, something about it doesn’t scratch the itch I have for the “perfect” Markdown-based note-taking interface.

So, what should a Markdown-loving, data-owning, multi-device user do? I’ve narrowed the options down to three popular self-hosted options that meet my criteria for note organization, cross-device sync, and end-to-end encryption.

This post isn’t about a final decision; it’s about the process. I’ll outline how I plan to test these apps, share my criteria, and invite you to follow along. A follow-up post will reveal my final choice, but first: the experiment.

Why a Self-Hosted Notes App?

Before we get into the specifics, let me share the values driving this search:

• Data Ownership: I want my notes on my server, not someone else’s.
• Cross-Device Access: I need to access notes on my MacBook and iPhone seamlessly.
• Longevity: I want my notes to be future-proof—accessible years from now in a simple format like Markdown.
• Simplicity: The interface needs to feel clean and intuitive. I want to focus on writing, not managing complexity.

Self-hosting aligns with these values, particularly when it comes to data ownership and syncing across devices. While self-hosting isn’t for everyone (there be dragons 🐉), I have a home server and the technical experience to make this work.

The Apps I’m Testing

Here are the three contenders that emerged from my research. They’re popular, Markdown-friendly, and support self-hosting with encryption:

• Joplin: A mature, open-source app with a rich feature set and a robust plugin ecosystem.
• Standard Notes: A privacy-first app with Proton-backed security, offering plain text, Markdown, and “Super Notes” for flexibility.
• Notesnook: The newest of the three, with a strong focus on encryption, usability, and a promising user base.

Joplin stands out for its longevity and flexibility. Its community and plugin support make it the most customizable option.

Standard Notes is laser-focused on privacy and has the added credibility of being backed by Proton, a company I respect for its commitment to security.

Notesnook is the underdog here, but thanks to its clean interface and modern design, it's already gaining fans from the Standard Notes community.

Designing the Experiment

1. Goal

The core question: Which app best supports my note-taking workflow while meeting my values?

2. Testing Criteria

Here’s the list of criteria I’ll use to evaluate each app:

• Ease of Use: Is the interface intuitive and pleasant to use?
• Note Organization: Support for folders, tags, and search.
• Markdown Support: How well does it handle formatting, outlines, and large Markdown files?
• Sync and Backup: How reliable is cross-device syncing and data recovery?
• Customization: Options for themes, plugins, or extensibility.
• Performance: Speed and responsiveness with a larger database of notes.
• Community and Development: How active is the app’s development? Is there a clear roadmap?

3. Datasets

To test these apps, I’ll use a mix of my current notes from Obsidian, and some generated Markdown notes. My focus will be on text-based notes—outlines, logs, and general writing—since that’s how I primarily take notes. PDFs, images, or tables aren’t part of my workflow, so I won’t test those features heavily.

4. Schedule

I’ll run this experiment over three phases:

• Phase 1: Set up each app, configure self-hosting, and import test data.
• Phase 2: Use each app exclusively for a week to test daily workflows like note-taking, searching, and syncing.
• Phase 3: Run specific tests like bulk search, exporting notes, and restoring backups.

Tools and Resources

I’ll track the results of my experiment in a simple table. Each app will have its own column, and each row will represent a specific criterion or test.

For the test datasets, I’ll use my existing Obsidian notes and supplement them with generated Markdown files to ensure there is enough content to test performance and search functionality.

Expected Challenges and Questions

One challenge I already foresee: getting attached to a single feature or piece of functionality in an app that otherwise doesn’t meet my needs. I’ve been there before—falling in love with one “shiny” feature and losing sight of the bigger picture.

To combat this, I’m adopting the writer’s mindset of “killing my darlings.” I won’t let any one feature cloud my judgment. The goal is simplicity—not perfection. At the end of this process, I’ll commit to one app that best aligns with my criteria and workflow.

Another challenge I expect to run into is feature overload. One of the main reasons I am stepping away from Obsidian is that I got overwhelmed by its vast plugin ecosystem. I suspect that I might encounter that in Joplin. I need to remind myself that more isn't always better for my workflow.

Lastly, since I am self-hosting, I wonder how reliable my system will be? How often do I need to anticipate running updates? Will there be application updates that break my workflow? Notesnook and Standard Notes both have subscription plans where they host the data. I know if there are updates that break anything, they will prioritize getting those fixed first. Should I have an alternative application I can plug notes into when if I temporarily lose access to the application of choice?

Invitation to You

What do you think of my process so far? Am I missing any key criteria or tests? Have you tried Joplin, Standard Notes, or Notesnook yourself? If so, what’s your experience been like?

If this experiment resonates with you, I’d love for you to join me. Let me know if you need help setting up any of these tools for self-hosting—I’m more than happy to share what I know.

Conclusion

This post marks the beginning of my journey to find the perfect self-hosted notes app. Over the next few weeks, I will test Joplin, Standard Notes, and Notesnook to determine which best supports my workflow and values.

While I don’t expect the perfect app to exist, I do expect to find the best fit for my needs. My criteria are set, my schedule is mapped out, and I’m excited to dive in.

Stay tuned for the follow-up post, where I’ll share the results of the experiment and reveal my final decision. Until then, I’d love to hear your thoughts—and if you’re conducting a similar search, let’s compare notes!

Let the testing begin! 🚀