diff --git a/pkgs/development/haskell-modules/configuration-common.nix b/pkgs/development/haskell-modules/configuration-common.nix
index 79a8beec01b1..777cbef33597 100644
--- a/pkgs/development/haskell-modules/configuration-common.nix
+++ b/pkgs/development/haskell-modules/configuration-common.nix
@@ -411,6 +411,13 @@ self: super: {
         rm -r $out/doc/?ndroid*
       '';
     };
+
+    patches = drv.patches or [ ] ++ [
+      # Prevent .desktop files from being installed to $out/usr/share.
+      # TODO(@sternenseemann): submit upstreamable patch resolving this
+      # (this should be possible by also taking PREFIX into account).
+      ./patches/git-annex-no-usr-prefix.patch
+    ];
   }) super.git-annex;
 
   # Too strict bounds on servant
diff --git a/pkgs/development/haskell-modules/patches/git-annex-no-usr-prefix.patch b/pkgs/development/haskell-modules/patches/git-annex-no-usr-prefix.patch
new file mode 100644
index 000000000000..03c9368d52fb
--- /dev/null
+++ b/pkgs/development/haskell-modules/patches/git-annex-no-usr-prefix.patch
@@ -0,0 +1,13 @@
+diff --git a/Utility/FreeDesktop.hs b/Utility/FreeDesktop.hs
+index 896b89b991..6cbb4f90ae 100644
+--- a/Utility/FreeDesktop.hs
++++ b/Utility/FreeDesktop.hs
+@@ -112,7 +112,7 @@ desktopfile f = f ++ ".desktop"
+ 
+ {- Directory used for installation of system wide data files.. -}
+ systemDataDir :: FilePath
+-systemDataDir = "/usr/share"
++systemDataDir = "/share"
+ 
+ {- Directory used for installation of system wide config files. -}
+ systemConfigDir :: FilePath