It is same no matter of fedora version.
You’ve been asking about it in How do I install Flathub Flatpaks on Fedora 38 XFCE? - #24 by Cosmic3ye and said it works in fc38xfce, then that it don’t work in fc41xfce and now you are here.
I think you can’t comprehend solution from many posts into one, so I’ll post one continuous terminal to show you that it works in fc42xfce and in other versions too.
First, run terminal in a template:
[user@fedora-42-xfce ~]$ sudo dnf install flatpak
Updating and loading repositories:
Repositories loaded.
Package Arch Version Repository Size
Installing:
flatpak x86_64 1.16.1-1.fc42 updates 6.5 MiB
Installing dependencies:
composefs-libs x86_64 1.0.8-2.fc42 fedora 146.2 KiB
flatpak-selinux noarch 1.16.1-1.fc42 updates 12.7 KiB
flatpak-session-helper x86_64 1.16.1-1.fc42 updates 99.2 KiB
malcontent-libs x86_64 0.13.0-2.fc42 fedora 112.7 KiB
ostree-libs x86_64 2025.6-1.fc42 updates 1.2 MiB
Installing weak dependencies:
p11-kit-server x86_64 0.25.8-1.fc42 updates 32.2 KiB
Transaction Summary:
Installing: 7 packages
Total size of inbound packages is 2 MiB. Need to download 2 MiB.
After this operation, 8 MiB extra will be used (install 8 MiB, remove 0 B).
Is this ok [y/N]: y
[1/7] malcontent-libs-0:0.13.0-2.fc42.x86_64 100% | 118.4 KiB/s | 47.0 KiB | 00m00s
[2/7] flatpak-session-helper-0:1.16.1-1.fc42.x86_64 100% | 81.4 KiB/s | 42.7 KiB | 00m01s
[3/7] composefs-libs-0:1.0.8-2.fc42.x86_64 100% | 192.1 KiB/s | 55.9 KiB | 00m00s
[4/7] flatpak-selinux-0:1.16.1-1.fc42.noarch 100% | 131.7 KiB/s | 22.1 KiB | 00m00s
[5/7] p11-kit-server-0:0.25.8-1.fc42.x86_64 100% | 180.1 KiB/s | 23.1 KiB | 00m00s
[6/7] flatpak-0:1.16.1-1.fc42.x86_64 100% | 1.4 MiB/s | 1.7 MiB | 00m01s
[7/7] ostree-libs-0:2025.6-1.fc42.x86_64 100% | 393.8 KiB/s | 485.1 KiB | 00m01s
--------------------------------------------------------------------------------------------------------------------------------------
[7/7] Total 100% | 281.0 KiB/s | 2.4 MiB | 00m09s
Running transaction
[1/9] Verify package files 100% | 583.0 B/s | 7.0 B | 00m00s
[2/9] Prepare transaction 100% | 18.0 B/s | 7.0 B | 00m00s
[3/9] Installing flatpak-selinux-0:1.16.1-1.fc42.noarch 100% | 444.0 B/s | 13.2 KiB | 00m30s
[4/9] Installing composefs-libs-0:1.0.8-2.fc42.x86_64 100% | 2.3 MiB/s | 148.0 KiB | 00m00s
[5/9] Installing ostree-libs-0:2025.6-1.fc42.x86_64 100% | 21.2 MiB/s | 1.2 MiB | 00m00s
[6/9] Installing malcontent-libs-0:0.13.0-2.fc42.x86_64 100% | 3.0 MiB/s | 114.4 KiB | 00m00s
[7/9] Installing flatpak-session-helper-0:1.16.1-1.fc42.x86_64 100% | 409.3 KiB/s | 100.7 KiB | 00m00s
>>> Running sysusers scriptlet: flatpak-0:1.16.1-1.fc42.x86_64
>>> Finished sysusers scriptlet: flatpak-0:1.16.1-1.fc42.x86_64
>>> Scriptlet output:
>>> Creating group 'flatpak' with GID 979.
>>> Creating user 'flatpak' (Flatpak system helper) with UID 979 and GID 979.
>>>
[8/9] Installing flatpak-0:1.16.1-1.fc42.x86_64 100% | 9.1 MiB/s | 6.5 MiB | 00m01s
>>> Running %post scriptlet: flatpak-0:1.16.1-1.fc42.x86_64
>>> Finished %post scriptlet: flatpak-0:1.16.1-1.fc42.x86_64
>>> Scriptlet output:
>>> Created symlink '/etc/systemd/system/multi-user.target.wants/flatpak-add-fedora-repos.service' → '/usr/lib/systemd/system/flatpak-
>>>
[9/9] Installing p11-kit-server-0:0.25.8-1.fc42.x86_64 100% | 3.1 KiB/s | 33.2 KiB | 00m11s
Complete!
You need to close this template for changes/installed app be saved.
Now you open appVM terminal (always remember to add --user option to every flatpak command - it’s not added at flathub site):
[user@disp2978 ~]$
[user@disp2978 ~]$ export http_proxy=127.0.0.1:8082
[user@disp2978 ~]$
[user@disp2978 ~]$ flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
Note that the directories
'/var/lib/flatpak/exports/share'
'/home/user/.local/share/flatpak/exports/share'
are not in the search path set by the XDG_DATA_DIRS environment variable, so
applications installed by Flatpak may not appear on your desktop until the
session is restarted.
[user@disp2978 ~]$
Now, still in appVM terminal install packages (remember about --user):
[user@disp9399 ~]$
[user@disp9399 ~]$ flatpak install --user flathub org.thonny.Thonny
Note that the directories
'/var/lib/flatpak/exports/share'
'/home/user/.local/share/flatpak/exports/share'
are not in the search path set by the XDG_DATA_DIRS environment variable, so
applications installed by Flatpak may not appear on your desktop until the
session is restarted.
Looking for matches…
Required runtime for org.thonny.Thonny/x86_64/stable (runtime/org.freedesktop.Sdk/x86_64/24.08) found in remote flathub
Do you want to install it? [Y/n]: y
org.thonny.Thonny permissions:
ipc network x11 devices file access [1] system dbus access [2]
[1] /media, /run/media, home
[2] org.freedesktop.UDisks2
ID Branch Op Remote Download
1. [✓] org.freedesktop.Platform.GL.default 24.08 i flathub 144.7 MB / 145.4 MB
2. [✓] org.freedesktop.Platform.GL.default 24.08extra i flathub 24.0 MB / 145.4 MB
3. [✗] org.freedesktop.Platform.openh264 2.5.1 i flathub 294.1 kB / 971.4 kB
4. [✓] org.freedesktop.Sdk.Locale 24.08 i flathub 191.4 MB / 393.2 MB
5. [✓] org.gtk.Gtk3theme.Adwaita-dark 3.22 i flathub 4.7 kB / 1.5 kB
6. [✓] org.freedesktop.Sdk 24.08 i flathub 548.3 MB / 630.5 MB
7. [✓] org.thonny.Thonny stable i flathub 18.9 MB / 26.7 MB
Warning: While downloading http://ciscobinary.openh264.org/libopenh264-2.5.1-linux64.7.so.bz2: While fetching http://ciscobinary.openh264.org/libopenh264-2.5.1-linux64.7.so.bz2: [7] Could not connect to server
Installation complete.
PS: Installing pyCharm is like ~1GB of dependencies and 1.3GB of IDE itself and my ISP is wonky today so installed Thony instead
PS2: been too lazy to make new template and appVM so made it in disposable