The Frustrating Part

Here’s what drives you crazy: you install Brave, maybe update it, and suddenly there are two Brave icons in your app menu. You launch one, it’s version 1.91.171. You launch the other, it’s an older 1.88.138. Which one is actually running? Why aren’t they the same?

I spent 20 minutes thinking I’d broken my package manager before I realized what was actually happening.

The Quick Fix (I Wished I’d Known Earlier)

Here’s exactly what I did to fix it:

1. Check what APT has installed:

apt list --installed | grep -i brave

2. Check if Flatpak snuck in an extra copy:

flatpak list | grep -i brave

3. When I saw the older version in Flatpak, I removed it:

flatpak uninstall com.brave.Browser

That’s it. One command fixed the whole mess.

What I Actually Did Step-by-Step

Step 1: I Checked APT First

I ran this to see what APT thought I had:

apt list --installed | grep -i brave

It showed me:

brave-browser/stable,now 1.91.171 amd64 [installed]
brave-keyring/stable,stable,now 1.19 all [installed]

So APT only knew about one Brave. That told me the duplicate wasn’t APT’s fault.

Then I checked where Brave lives:

which brave-browser

Got back /usr/bin/brave-browser – exactly where it should be.

Step 2: I Checked Flatpak (And Found The Culprit)

Here’s where I caught the problem. I ran:

flatpak list | grep -i brave

And bam:

Brave  com.brave.Browser  1.88.138  stable  system

That older version (1.88.138) was the ghost in my machine. Flatpak had installed its own Brave completely separate from APT.

No wonder I had two copies.

Step 3: I Nuked The Old Flatpak Version

I ran:

flatpak uninstall com.brave.Browser

Typed y when it asked, and it was gone.

Step 4: I Made Sure It Actually Worked

Always double-check. I ran:

flatpak list | grep -i brave

Got nothing back. Perfect.

Then I checked my real Brave version:

brave-browser --version

Brave Browser 1.91.171

Fixed.

Step 5: That Annoying Spotify Warning (Ignore It Or Fix It)

During all this, APT kept yelling about:

NO_PUBKEY 5384CE82BA52C83A

I almost chased this thinking it was the problem. It’s not. It’s just Spotify’s repository key being outdated. Brave updated just fine.

I don’t use Spotify anymore, so I just removed the repo:

sudo rm /etc/apt/sources.list.d/spotify.list
sudo apt update

Step 6: One Last Update For Good Measure

APT told me brave-keyring could update from 1.19 to 1.20, so I ran:

sudo apt update
sudo apt upgrade

Final Summary and Tips

Root Cause

The duplicate Brave installation was not caused by a failed Brave upgrade. The browser had been installed from two different package sources:

• APT version: 1.91.171
• Flatpak version: 1.88.138

Solution

Identify the duplicate source:

flatpak list | grep -i brave

Remove the outdated Flatpak installation:

flatpak uninstall com.brave.Browser

Verify only one version remains:

brave-browser --version

Key Takeaway

When Linux applications appear to be installed twice, don’t assume the package manager is broken. First check whether the application exists in multiple package ecosystems (APT, Flatpak, or Snap). In many cases, the duplicate installation is simply the same application installed from different sources.