The Store version of OneNote is the future on Windows, but you don't have to stop using the desktop version and it will keep getting bug fixes.
The 'hot ideas' section in the OneNote for Windows UserVoice is currently headed by requests (14 out of the top 20 suggestions) to either add all the missing features from OneNote 2016 to the Store version of the app or just keep shipping the desktop version. Despite appearances to the contrary (like a bug that automatically uninstalled OneNote 2016 when you installed one particular version of Office 2019), Microsoft is committed to doing both.
There are plenty of features the Store version of OneNote doesn't have yet: the ability to send a copy of a page by email; paste multiple images at once; create custom AutoCorrect options; rotate printouts; pin your favourite tools to the quick access toolbar; send clips directly to OneNote without having to spend time finding the section you want; or work with a notebook stored on a network drive instead of in the cloud, for example. If any of those are features you need, you can keep using OneNote 2016.
The desktop version isn't getting any new features (so the new fast sync engine and automatic sync of custom tags won't come to desktop OneNote) and you'll have to put up with Microsoft telling you that you're not using the 'best' version of OneNote and 'strongly encouraging' you to switch.
But despite the nagging, you can carry on using OneNote 2016 without worrying that it's going to stop working. You can carry on reporting bugs and they'll get fixed; security updates and support will be available until October 13, 2020 for mainstream support and October 14, 2025 for extended support. That's longer than support for Windows 7, where OneNote 2016 is the only option apart from OneNote Online.
So the desktop version isn't 'dead' or deprecated: OneNote 2016 may be the legacy version, but Microsoft video president and technical fellow for 'Notes and Tasks' (NoTa) Laura Butler also calls it the 'mainstream' version.
The OneNote team is very aware that there are a lot of features missing from the Store version of OneNote, and in most cases the plan is not just to match the desktop features but to improve on them. So custom tags have been in desktop OneNote for a long time, but you had to add them on every new PC you used; when you add them in the Store version, they sync automatically (although you can't yet assign them to keyboard shortcuts).
After that there are new features planned, like much richer tools for sending content from other applications and a better interface for managing notebook sections and sub-pages. Butler teased future plans and priorities for the Notes and Tasks group on Twitter, appropriately enough as a capture of her own OneNote notebooks. The modern version of OneNote is about half finished, and while this work continues desktop OneNote isn't dead.
SEE: Windows 10 power tips: Secret shortcuts to your favorite settings (Tech Pro Research)
One desktop feature isn't going to be in the Store version — or on Macs or smartphones: the ability to keep notebooks on your own PC or a network drive (which lets you sync notes between devices, but only when they're connected to that network). That's a popular feature, but for the Store version of OneNote the only options will be cloud storage or the on-premises version of SharePoint (which hosts OneDrive). That's because the new sync engine needs the cloud connection for things like versioning.
There's no equivalent of the Group Policy controls for OneNote 2016 either (you can find those in the Administrative Template files for Office). It's not clear if there will be MDM equivalents for controlling OneNote for Windows 10 as more features are added; so far the admin experience is more about allowing teachers to create and distribute staff notebooks through SharePoint and make student homework in OneNote read-only once it's been marked.
Is Microsoft automatically uninstalling OneNote?
Office 2019 makes OneNote for Windows 10 the default; Office 365 ProPlus also makes it the default, and from January 2019 that applies to all update channels, including the Semi-Annual Channel that goes to mainstream business users.
If you install Office 2019 or Office 365 (including Office 365 ProPlus and Business) on a new PC, that won't include OneNote 2016. If you upgrade from Office 2016 (or 2013) to Office 2019 and you have desktop OneNote installed, it should stay on your PC. One specific Office update in September 2018 (version 16.0.10730.20088) uninstalled OneNote 2016; Microsoft says that was a bug that affected only a small percentage of users and that subsequent updates won't uninstall OneNote.
But the Office 2019 upgrade also pushes 'upgrading' from 32-bit to 64-bit. That's good for handling larger Excel spreadsheets, and — because Office 2019 uses Click-To-Run rather than an MSI — it's seamless. But it means the upgrade actually uninstalls Office, reinstalls it and migrates your settings — and that uninstalls OneNote 2016 but doesn't reinstall it.
If you're an admin, you can configure the Office image you use for deployment to include OneNote 2016, even if you're moving to 64-bit Office; if you use the Office Deployment Tool to deploy Office 365 ProPlus, OneNote 2016 will be installed by default. If OneNote 2016 isn't installed but Office 365 ProPlus is, deploying it with the Office Deployment tool will add OneNote without reinstalling the rest of Office.
If you're using the Office 365 Installer in Configuration Manager, older versions include OneNote 2016 by default. But if you're using the Current Branch, OneNote 2016 will be excluded by default, so you'll need to choose it explicitly in the Office 365 Installer UI.
If you're a user (or you're setting up Office on user machines by installing it from the Office 365 portal), you can install OneNote directly, and there are different ways to do this. If you're moving to 64-bit Office, make sure you get the 64-bit version; if you're not sure, use File / Account / About Word to check whether you have 32-bit or 64-bit Office installed. You'll also need 64-bit versions of any OneNote plugins you use, like the excellent Onetastic.
If you're sticking to 32-bit Office, you can download the 32-bit version of OneNote 2016.
SEE: System update policy template download (Tech Pro Research)
If you have a paid licence for Office, you get extra features in OneNote (like the ability to open local notebooks). If you install OneNote 2016 before you install and activate Office 2019 or Office 365, it will install with the Home and Student licence, which doesn't include those features. Once you install and activate Office, OneNote will pick up the full licence and enable the extra features, but you may still see the licence displayed as Home and Student. To avoid that, make sure Office is activated before installing OneNote.
But if you want the advantages of getting desktop OneNote as if it was a Store app, you can get OneNote 2016 from the Microsoft store. This is a preview of the Centennial version of OneNote and it has some limitations (you can't use add-ins like Onetastic yet, for example) and you can only get it using the direct link because it doesn't show up when you search the Store for OneNote. But if you're using the Microsoft Store to get the other desktop Office applications, you can do the same for OneNote.
Organizations that block the Microsoft Store can set up Microsoft Store for Business and whitelist applications like OneNote 2016 that they want to make available.
While you're sticking with desktop OneNote, you can uninstall the OneNote app if you don't want to try it out as long as you have Windows 10 1809 installed.
If you do use both versions there are some things to watch out for. The Store version of OneNote doesn't share notebook files with OneNote desktop, so if you open a notebook in both applications, you'll be storing and syncing it twice (for a large notebook, that can take up a lot of space). And if you record audio in the Store version of OneNote, you can't play that back in OneNote 2016 because it uses a different audio format (a breaking change Microsoft could fix by giving users a choice of audio formats in the Store version of OneNote). Making it easier to use both versions of OneNote together would make it easier for users to move to the Windows 10 version of OneNote for some tasks and only go back to OneNote 2016 for those last few features they need.
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