diff --git a/pkgs/applications/misc/yubioath-desktop/default.nix b/pkgs/applications/misc/yubioath-desktop/default.nix
deleted file mode 100644
index 8a1645239082..000000000000
--- a/pkgs/applications/misc/yubioath-desktop/default.nix
+++ /dev/null
@@ -1,76 +0,0 @@
-{ lib
-, stdenv
-, fetchurl
-, mkDerivation
-, qmake
-, qtbase
-, qtquickcontrols2
-, qtgraphicaleffects
-, qtmultimedia
-, python3
-, pyotherside
-, pcsclite
-, yubikey-personalization
-, yubikey-manager
-, makeWrapper
-}:
-
-mkDerivation rec {
-  pname = "yubioath-desktop";
-  version = "5.1.0";
-
-  src = fetchurl {
-    url = "https://developers.yubico.com/yubioath-desktop/Releases/yubioath-desktop-${version}.tar.gz";
-    hash = "sha256-Lm9F4eaG9T5brAV7XDAkoj0WClmXEYIhuUzh2rk0oc0=";
-  };
-
-  doCheck = false;
-
-  buildInputs = [ qtbase qtquickcontrols2 qtgraphicaleffects qtmultimedia python3 ];
-
-  nativeBuildInputs = [ qmake makeWrapper python3.pkgs.wrapPython ];
-
-  postPatch = ''
-    substituteInPlace QZXing/QZXing-components.pri \
-      --replace 'target.path = $$PREFIX/lib' 'target.path = $$PREFIX/bin'
-  '';
-
-  pythonPath = [ yubikey-manager ];
-
-  # Need LD_PRELOAD for libykpers as the Nix cpython disables ctypes.cdll.LoadLibrary
-  # support that the yubicommon library uses to load libykpers
-
-  postInstall = ''
-    buildPythonPath "$out $pythonPath"
-    wrapProgram $out/bin/yubioath-desktop \
-      --prefix PYTHONPATH : "$program_PYTHONPATH" \
-      --prefix QML2_IMPORT_PATH : "${pyotherside}/${qtbase.qtQmlPrefix}" \
-      --prefix LD_PRELOAD : "${yubikey-personalization}/lib/libykpers-1.so" \
-      --prefix LD_LIBRARY_PATH : "${lib.getLib pcsclite}/lib:${yubikey-personalization}/lib"
-
-      mkdir -p $out/share/applications
-      cp resources/com.yubico.yubioath.desktop \
-        $out/share/applications/com.yubico.yubioath.desktop
-      mkdir -p $out/share/yubioath/icons
-      cp resources/icons/*.{icns,ico,png,svg} $out/share/yubioath/icons
-      substituteInPlace $out/share/applications/com.yubico.yubioath.desktop \
-        --replace 'Exec=yubioath-desktop' "Exec=$out/bin/yubioath-desktop" \
-        --replace 'Icon=com.yubico.yubioath' "Icon=$out/share/yubioath/icons/com.yubico.yubioath.png"
-  '';
-
-  meta = with lib; {
-    description = "Yubico Authenticator";
-    longDescription = ''
-      Application for generating Open Authentication (OATH) time-based TOTP and
-      event-based HOTP one-time password codes, with the help of a YubiKey that
-      protects the shared secrets.
-    '';
-
-    homepage = "https://developers.yubico.com/yubioath-desktop";
-    downloadPage = "https://developers.yubico.com/yubioath-desktop/Releases/";
-    changelog = "https://developers.yubico.com/yubioath-desktop/Release_Notes.html";
-
-    license = lib.licenses.bsd2;
-    maintainers = with maintainers; [ mic92 risson ];
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 3ce97f6b505b..65693df18a89 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1629,6 +1629,7 @@ mapAliases ({
   youtubeDL = throw "'youtubeDL' has been renamed to/replaced by 'youtube-dl'"; # Converted to throw 2022-02-22
   ytop = throw "ytop has been abandoned by upstream. Consider switching to bottom instead";
   yubikey-neo-manager = throw "yubikey-neo-manager has been removed because it was broken. Use yubikey-manager-qt instead"; # Added 2021-03-08
+  yubioath-desktop = throw "yubioath-desktop has been deprecated by upstream in favor of https://github.com/Yubico/yubioath-flutter"; # Added 2022-11-22
   yuzu-ea = yuzu-early-access; # Added 2022-08-18
   yuzu = yuzu-mainline; # Added 2021-01-25
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 79c2c964e137..1ee63cffff4a 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23102,8 +23102,6 @@ with pkgs;
 
   yojimbo = callPackage ../development/libraries/yojimbo { };
 
-  yubioath-desktop = libsForQt5.callPackage ../applications/misc/yubioath-desktop { };
-
   yubico-pam = callPackage ../development/libraries/yubico-pam { };
 
   yubico-piv-tool = callPackage ../tools/misc/yubico-piv-tool {