diff --git a/pkgs/development/tools/build-managers/meson/clear-old-rpath.patch b/pkgs/development/tools/build-managers/meson/clear-old-rpath.patch
new file mode 100644
index 00000000000..0a52fe60e9d
--- /dev/null
+++ b/pkgs/development/tools/build-managers/meson/clear-old-rpath.patch
@@ -0,0 +1,20 @@
+diff --git a/mesonbuild/scripts/depfixer.py b/mesonbuild/scripts/depfixer.py
+index 77ac03d66..d12f77592 100644
+--- a/mesonbuild/scripts/depfixer.py
++++ b/mesonbuild/scripts/depfixer.py
+@@ -337,6 +337,15 @@ class Elf(DataSizes):
+         if not new_rpath:
+             self.remove_rpath_entry(entrynum)
+         else:
++            # Clear old rpath to avoid stale references,
++            # not heeding the warning above about de-duplication
++            # since it does not seem to cause issues for us
++            # and not doing so trips up Nix’s reference checker.
++            # See https://github.com/NixOS/nixpkgs/pull/46020
++            # and https://github.com/NixOS/nixpkgs/issues/95163
++            self.bf.seek(rp_off)
++            self.bf.write(b'\0'*len(old_rpath))
++
+             self.bf.seek(rp_off)
+             self.bf.write(new_rpath)
+             self.bf.write(b'\0')
diff --git a/pkgs/development/tools/build-managers/meson/default.nix b/pkgs/development/tools/build-managers/meson/default.nix
index dad1dfa360c..c32635d80e1 100644
--- a/pkgs/development/tools/build-managers/meson/default.nix
+++ b/pkgs/development/tools/build-managers/meson/default.nix
@@ -43,6 +43,14 @@ python3.pkgs.buildPythonApplication rec {
       src = ./fix-rpath.patch;
       inherit (builtins) storeDir;
     })
+
+    # When Meson removes build_rpath from DT_RUNPATH entry, it just writes
+    # the shorter NUL-terminated new rpath over the old one to reduce
+    # the risk of potentially breaking the ELF files.
+    # But this can cause much bigger problem for Nix as it can produce
+    # cut-in-half-by-\0 store path references.
+    # Let’s just clear the whole rpath and hope for the best.
+    ./clear-old-rpath.patch
   ];
 
   setupHook = ./setup-hook.sh;