The best open source alternative to Flatpak is Homebrew. If that doesn't suit you, our users have ranked more than 10 alternatives to Flatpak and 16 is open source so hopefully you can find a suitable replacement. Other interesting open source alternatives to Flatpak are Snapcraft (Free, Open Source), Advanced Package Tool (Free, Open Source), GNU Guix (Free, Open Source) and Zero Install (Free, Open Source).
Snaps are software packages that are simple to create and install. They auto-update and are safe to run. And because they bundle their dependencies, they work on all major Linux systems without modification.
Almost everyone thinks Snapcraft is a great alternative to Flatpak.
Zero Install is a decentralised cross-distribution software installation system. Other features include full support for shared libraries, sharing between users, and integration with native platform package managers.