NotebookLM has become one of my most-used tools because it’s insanely good at making sense of messy inputs and long documents. Sometimes it feels almost unfair when it’s working at full power. But no tool is 100% perfect, and the more you use NotebookLM, the more you notice some friction points.

This is why I started bringing Joplin into the mix. It’s one of my top note-taking apps, and although it doesn’t have the synthesizing power of NotebookLM, it has something the AI lacks - organization. It’s a super clean and functional tool that I would recommend to anyone who wants a local open-source app to manage their notes. Here’s why I’ve brought it on board my research and note-taking stack, and how it fills in NotebookLM’s gaps…

What is NotebookLM’s biggest problem?

It’s such a simple but major function

While NotebookLM is probably my top tool of the last couple of years, it has one major problem - it doesn’t have proper organizational features. I’m specifically talking about organization inside your notebooks, but it also lacks structure in the notebook dashboard, so the disorganization shows up at every level of the app. Notebooks are laid out individually on the homepage with no way to drag or group them.

And then there’s the content in the notebooks themselves, which is my biggest frustration with NotebookLM. Sources are listed in alphabetical order by default and there’s no way to drag them around, which is why I started relying on a renaming system. There are some sources I select and deselect constantly, so I prefix them with numbers 01, 02, 03, etc. to keep them in the order I want without having to look for them in the source panel all the time.

Same thing with content in the studio panel - you can’t drag them. Whichever mind map or note you created or opened most recently bounces to the top, and that’s the order you’re stuck with. There are also no tags, so I’ve resorted to manually adding “tags” in the note titles (using the hashtag character #) so they’re in my line of sight.

This is why some NotebookLM users, including myself, don’t consider NotebookLM a real notes app, because proper note-taking apps give you some basic customization. And it’s also why Gistr is right on NotebookLM’s tail, because it does actually give you real, block-based note-taking features, complete with a slash command and formatting options. The AI just isn’t as powerful as NotebookLM (yet).

What is Joplin?

And why is it the ideal way to organize your NotebookLM content?

Joplin is a free open-source note-taking app that’s lightweight, cross-platform, easy to use, and can fit in just about anyone’s note-taking stack. The cool thing about Joplin is that it also has a notebook system, but the way it’s structured is different from NotebookLM. For starters, there is no home dashboard - instead your notebooks show up on the left panel, and then they expand to the right in a hierarchical folder structure. I don’t even really mind that NotebookLM doesn’t follow this exact layout, but any type of grouping structure would improve the UX.

And in Joplin, you can completely customize your notes. They’re draggable, linkable, and taggable. It works really well with NotebookLM because Joplin exports locally, which can easily sync with your Google Drive, which integrates with NotebookLM. And it’s also a Markdown and rich text hybrid, so adding NotebookLM's responses retains the formatting.

How I use Joplin to organize what NotebookLM can’t

It’s dead simple

I will give props to NotebookLM for being super easy to navigate, and I’m guessing that the lack of organization features might actually be because Google wants to keep the app as minimal as possible. But until it finds a way to incorporate more structure, I’m sticking with Joplin, which is also easy and intuitive to navigate, but with better organization. So using these two together works seamlessly.

I start with my usual workflow in NotebookLM, which includes adding sources, creating mind maps and quizzes, and then prompting the AI to help me with learning and studying. In Joplin, I’ve created a couple of notebooks that reflect the ones I have in NotebookLM, such as UX design and psychology, and each page explores a different topic in those areas. And then, as I’m working in NotebookLM, I’ll just copy over some of the best responses and key notes.

I do this manually because there is no automation, but setting that up would likely be more effort than it’s worth anyway - this is what the Copy button is for in NotebookLM. When NotebookLM gives me a response that I know I’m going to refer back to later, I copy-paste it into a relevant note in Joplin. It retains the formatting just as it was in NotebookLM, including tables.

Then I simply use Joplin as it’s intended. I expand on the responses with my own notes, create tags for instant references, and most importantly, drag the notes around in my notebooks in an order than makes sense. I can also interlink notes with one another to create a personal knowledge base. Furthermore, I export some of them to my local notes folder that’s synced with Google Drive, which I can add as sources in other notebooks in NotebookLM.

Joplin solves NotebookLM’s biggest flaw

NotebookLM has one of the most powerful AIs but completely lacks structure. While Joplin lacks the second-brain AI element, it gives you proper folder organization and tags for your notebooks. But using them together taps into the best of both, and it solves NotebookLM’s biggest flaw.