When comparing Flatpak vs Nix, the Slant community recommends Nix for most people. In the question“What are the best Linux package managers?” Nix is ranked 6th while Flatpak is ranked 18th. The most important reason people chose Nix is:
Nix is a purely functional package management system. This means that the act of building a package does not have side effects, such as destructively updating or deleting files that may be used by other packages.
Specs
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Pros
Pro Cross-distribution
You can install flatpak packages on any distro you want.
Pro fast
searching, installing and updating are faster than others in my experience
Pro Doesn't bog system down like snaps.
Plus it's not proprietary.
Pro Application sandboxing
All applications are limited to a set of predefined permissions, enhancing privacy and security.
Pro A well-written documentation
Pro Flexible runtime management
You can install a lot of runtimes for different apps, making applications a lot more compatible while still allowing some applications to share their runtimes.
Pro No side effects when building packages
Nix is a purely functional package management system. This means that the act of building a package does not have side effects, such as destructively updating or deleting files that may be used by other packages.
Pro Isolated development environments
Nix allows the creation of project-specific shell and build environments which are isolated from the rest of the system. These environments are defined declaratively to ensure reproducibility.
Pro Can replace docker in some places
Pro Can use multiple versions of the same package
Because of the functional approach it takes, Nix makes it easy for systems to use multiple versions of the same package simultaneously, and ensure that updating or removing a package can't break other packages.
Pro The configuration works on "All machines"
No more of the traditional: "it works on my machine". When it says reproducible, this is the real deal.
Cons
Con Bloated
Due to the way Flatpack handles packaging, this can lead to a large cache being created which quickly inflates to unreasonable sizes. Not only this, but using flatpack requires a large chunk of space to be reserved for it's own file hierarchy.
Con Difficult to export packages
It is difficult and convoluted to export installed packages and move to another system.
Con Doesn't work well with CLI programs
Invoking CLI programs can be a pain. From the weird reverse DNS package names to difficulty in easily managing container environment.
Con Does not work well for services on non-NixOS systems
When using Nix with anything other than NixOS you can run into difficulties with trying to start up services. For example, you can install docker with Nix, but it won't integrate with the host system's systemd leaving you to handcraft awkward workarounds in order to start the background service that docker requires. This seems like a critical flaw when using Nix on anything that is not NixOS, and it's unfortunate because this affects many of the packages many users would be most interested in using Nix to handle.
Con Steep learning curve
Con Cannot handle filetypes that have different semantics across different versions
While the functional approach that Nix takes is great for sandboxing binary artifacts of packages, it seriously lacks any power in handling configuration files or user data. It's difficult to upgrade and downgrade files where semantics and syntax can change between versions. Especially in Debian/Ubuntu it can cause severe problems where the upgrade process blocks and the user needs to resolve the 3-way merge.