diff --git a/pkgs/build-support/cc-wrapper/add-flags.sh b/pkgs/build-support/cc-wrapper/add-flags.sh
index cd5396f45f8b..838b963ead7b 100644
--- a/pkgs/build-support/cc-wrapper/add-flags.sh
+++ b/pkgs/build-support/cc-wrapper/add-flags.sh
@@ -95,11 +95,6 @@ if [ "@darwinMinVersion@" ]; then
     # xcbuild needs `SDKROOT` to be the name of the SDK, which it sets in its own wrapper,
     # but compilers expect it to point to the absolute path.
     SDKROOT="$DEVELOPER_DIR/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"
-
-    # Set up various library paths since compilers may not support (or may have disabled) finding them in the sysroot.
-    NIX_CFLAGS_COMPILE_BEFORE_@suffixSalt@+=" -isysroot $SDKROOT"
-    NIX_CFLAGS_COMPILE_@suffixSalt@+=" -idirafter $SDKROOT/usr/include"
-    NIX_CFLAGS_COMPILE_@suffixSalt@+=" -iframework $SDKROOT/System/Library/Frameworks"
 fi
 
 # That way forked processes will not extend these environment variables again.
diff --git a/pkgs/development/compilers/llvm/common/clang/default.nix b/pkgs/development/compilers/llvm/common/clang/default.nix
index 5c9662c24d58..4bf30400832a 100644
--- a/pkgs/development/compilers/llvm/common/clang/default.nix
+++ b/pkgs/development/compilers/llvm/common/clang/default.nix
@@ -81,13 +81,17 @@ let
       # Make sure clang passes the correct location of libLTO to ld64
       substituteInPlace lib/Driver/ToolChains/Darwin.cpp \
         --replace-fail 'StringRef P = llvm::sys::path::parent_path(D.Dir);' 'StringRef P = "${lib.getLib libllvm}";'
-    '' + (if lib.versionOlder release_version "13" then ''
-      sed -i -e 's/DriverArgs.hasArg(options::OPT_nostdlibinc)/true/' \
-             -e 's/Args.hasArg(options::OPT_nostdlibinc)/true/' \
-             lib/Driver/ToolChains/*.cpp
-    '' else ''
-      (cd tools && ln -s ../../clang-tools-extra extra)
-    '') + lib.optionalString stdenv.hostPlatform.isMusl ''
+    '' + (
+      # See the comment on the `add-nostdlibinc-flag.patch` patch in
+      # `../default.nix` for why we skip Darwin here.
+      if lib.versionOlder release_version "13" && (!stdenv.hostPlatform.isDarwin || !stdenv.targetPlatform.isDarwin) then ''
+        sed -i -e 's/DriverArgs.hasArg(options::OPT_nostdlibinc)/true/' \
+               -e 's/Args.hasArg(options::OPT_nostdlibinc)/true/' \
+               lib/Driver/ToolChains/*.cpp
+      '' else ''
+        (cd tools && ln -s ../../clang-tools-extra extra)
+      ''
+    ) + lib.optionalString stdenv.hostPlatform.isMusl ''
       sed -i -e 's/lgcc_s/lgcc_eh/' lib/Driver/ToolChains/*.cpp
     '';
 
diff --git a/pkgs/development/compilers/llvm/common/default.nix b/pkgs/development/compilers/llvm/common/default.nix
index eaba6f45edfe..c3a98c1f063f 100644
--- a/pkgs/development/compilers/llvm/common/default.nix
+++ b/pkgs/development/compilers/llvm/common/default.nix
@@ -529,8 +529,24 @@ let
             # mis-compilation in firefox.
             # See: https://bugzilla.mozilla.org/show_bug.cgi?id=1741454
             (metadata.getVersionFile "clang/revert-malloc-alignment-assumption.patch")
+          # This patch prevents global system header directories from
+          # leaking through on non‐NixOS Linux. However, on macOS, the
+          # SDK path is used as the sysroot, and forcing `-nostdlibinc`
+          # breaks `-isysroot` with an unwrapped compiler. As macOS has
+          # no `/usr/include`, there’s essentially no risk to skipping
+          # the patch there. It’s possible that Homebrew headers in
+          # `/usr/local/include` might leak through to unwrapped
+          # compilers being used without an SDK set or something, but
+          # it hopefully shouldn’t matter.
+          #
+          # TODO: Figure out a better solution to this whole problem so
+          # that we won’t have to choose between breaking unwrapped
+          # compilers breaking libclang when we can do Linux‐to‐Darwin
+          # cross‐compilation again.
+          ++ lib.optional (
+            !args.stdenv.hostPlatform.isDarwin || !args.stdenv.targetPlatform.isDarwin
+          ) ./clang/add-nostdlibinc-flag.patch
           ++ [
-            ./clang/add-nostdlibinc-flag.patch
             (substituteAll {
               src =
                 if (lib.versionOlder metadata.release_version "16") then
diff --git a/pkgs/stdenv/darwin/default.nix b/pkgs/stdenv/darwin/default.nix
index 5a3ef15e392d..070d5ec23851 100644
--- a/pkgs/stdenv/darwin/default.nix
+++ b/pkgs/stdenv/darwin/default.nix
@@ -133,6 +133,17 @@ let
                 ln -s "${compiler-rt.out}/lib"   "$rsrc/lib"
                 ln -s "${compiler-rt.out}/share" "$rsrc/share"
                 echo "-resource-dir=$rsrc" >> $out/nix-support/cc-cflags
+              ''
+              + lib.optionalString (isFromBootstrapFiles prevStage.llvmPackages.clang-unwrapped) ''
+                # Work around the `-nostdlibinc` patch in the bootstrap tools.
+                # TODO: Remove after the bootstrap tools have been updated.
+                substituteAll ${builtins.toFile "add-flags-extra.sh" ''
+                  if [ "@darwinMinVersion@" ]; then
+                    NIX_CFLAGS_COMPILE_@suffixSalt@+=" -idirafter $SDKROOT/usr/include"
+                    NIX_CFLAGS_COMPILE_@suffixSalt@+=" -iframework $SDKROOT/System/Library/Frameworks"
+                  fi
+                ''} add-flags-extra.sh
+                cat add-flags-extra.sh >> $out/nix-support/add-flags.sh
               '';
 
             cc = prevStage.llvmPackages.clang-unwrapped;