diff --git a/conan/tools/apple/xcodetoolchain.py b/conan/tools/apple/xcodetoolchain.py
index 76d8c79180a..d46dca4cd17 100644
--- a/conan/tools/apple/xcodetoolchain.py
+++ b/conan/tools/apple/xcodetoolchain.py
@@ -51,7 +51,8 @@ def generate(self):
         save(self._agreggated_xconfig_filename, self._agreggated_xconfig_content)
         save(self._vars_xconfig_filename, self._vars_xconfig_content)
         if self._check_if_extra_flags:
-            save(self._flags_xcconfig_filename, self._flags_xcconfig_content)
+            save(self._flags_props_xconfig_filename, self._flags_xcconfig_content)
+            save(self._flags_xcconfig_filename, self._flags_xcconfig_aggregated_content)
         save(GLOBAL_XCCONFIG_FILENAME, self._global_xconfig_content)
 
     @property
@@ -118,13 +119,28 @@ def _check_if_extra_flags(self):
 
     @property
     def _flags_xcconfig_content(self):
-        defines = "GCC_PREPROCESSOR_DEFINITIONS = $(inherited) {}".format(" ".join(self._global_defines)) if self._global_defines else ""
-        cflags = "OTHER_CFLAGS = $(inherited) {}".format(" ".join(self._global_cflags)) if self._global_cflags else ""
-        cppflags = "OTHER_CPLUSPLUSFLAGS = $(inherited) {}".format(" ".join(self._global_cxxflags)) if self._global_cxxflags else ""
-        ldflags = "OTHER_LDFLAGS = $(inherited) {}".format(" ".join(self._global_ldflags)) if self._global_ldflags else ""
+        # Conditioned like the vars props file, so flags from different installed
+        # (config, arch, sdk) combinations don't overwrite each other.
+        condition = _xcconfig_conditional(self._conanfile.settings, self.configuration)
+        defines = "GCC_PREPROCESSOR_DEFINITIONS{} = $(inherited) {}".format(condition, " ".join(self._global_defines)) if self._global_defines else ""
+        cflags = "OTHER_CFLAGS{} = $(inherited) {}".format(condition, " ".join(self._global_cflags)) if self._global_cflags else ""
+        cppflags = "OTHER_CPLUSPLUSFLAGS{} = $(inherited) {}".format(condition, " ".join(self._global_cxxflags)) if self._global_cxxflags else ""
+        ldflags = "OTHER_LDFLAGS{} = $(inherited) {}".format(condition, " ".join(self._global_ldflags)) if self._global_ldflags else ""
         ret = self._flags_xconfig.format(defines=defines, cflags=cflags, cppflags=cppflags, ldflags=ldflags)
         return ret
 
+    @property
+    def _flags_props_xconfig_filename(self):
+        return "conan_global_flags{}{}".format(_xcconfig_settings_filename(self._conanfile.settings,
+                                                                            self.configuration),
+                                               self.extension)
+
+    @property
+    def _flags_xcconfig_aggregated_content(self):
+        return _add_includes_to_file_or_create(self._flags_xcconfig_filename,
+                                               self._agreggated_xconfig,
+                                               [self._flags_props_xconfig_filename])
+
     @property
     def _flags_xcconfig_filename(self):
         return "conan_global_flags" + self.extension
diff --git a/test/integration/toolchains/apple/test_xcodetoolchain.py b/test/integration/toolchains/apple/test_xcodetoolchain.py
index 8941f162beb..4f8c2844175 100644
--- a/test/integration/toolchains/apple/test_xcodetoolchain.py
+++ b/test/integration/toolchains/apple/test_xcodetoolchain.py
@@ -58,31 +58,52 @@ def test_toolchain_files(configuration, os_version, cppstd, libcxx, arch, sdk_ve
         assert 'CLANG_CXX_LANGUAGE_STANDARD{}={}'.format(condition, clang_cppstd) in toolchain_vars
 
 
+@pytest.mark.skipif(platform.system() != "Darwin", reason="Only for MacOS")
 def test_toolchain_flags():
     client = TestClient()
     client.save({"conanfile.txt": "[generators]\nXcodeToolchain\n"})
-    cmd = "install . -c 'tools.build:cxxflags=[\"flag1\"]' " \
-          "-c 'tools.build:defines=[\"MYDEFINITION\"]' " \
-          "-c 'tools.build:cflags=[\"flag2\"]' " \
-          "-c 'tools.build:sharedlinkflags=[\"flag3\"]' " \
-          "-c 'tools.build:exelinkflags=[\"flag4\"]'"
+    cmd = "install . -s build_type=Release -s arch=x86_64 " \
+          "-c 'tools.build:cxxflags=[\"cxxflags_release\"]' " \
+          "-c 'tools.build:defines=[\"defines_release\"]' " \
+          "-c 'tools.build:cflags=[\"cflags_release\"]' " \
+          "-c 'tools.build:sharedlinkflags=[\"sharedlinkflags_release\"]' " \
+          "-c 'tools.build:exelinkflags=[\"exelinkflags_release\"]'"
     client.run(cmd)
+    filename = _get_filename("Release", "x86_64", None)
+    condition = _condition("Release", "x86_64", None)
+
+    conan_global_flags_props = client.load("conan_global_flags{}.xcconfig".format(filename))
+    assert "GCC_PREPROCESSOR_DEFINITIONS{} = $(inherited) defines_release".format(condition) in conan_global_flags_props
+    assert "OTHER_CFLAGS{} = $(inherited) cflags_release".format(condition) in conan_global_flags_props
+    assert "OTHER_CPLUSPLUSFLAGS{} = $(inherited) cxxflags_release".format(condition) in conan_global_flags_props
+    assert "OTHER_LDFLAGS{} = $(inherited) sharedlinkflags_release exelinkflags_release".format(condition) in conan_global_flags_props
+
+    # A second install, for a different configuration, must not overwrite the
+    # first one's flags -- each stays reachable under its own condition.
+    client.run("install . -s build_type=Debug -s arch=x86_64 -c 'tools.build:cxxflags=[\"cxxflags_debug\"]'")
+    debug_filename = _get_filename("Debug", "x86_64", None)
+    debug_flags = client.load("conan_global_flags{}.xcconfig".format(debug_filename))
+    assert "cxxflags_debug" in debug_flags
+    assert "cxxflags_release" not in debug_flags
+
     conan_global_flags = client.load("conan_global_flags.xcconfig")
-    assert "GCC_PREPROCESSOR_DEFINITIONS = $(inherited) MYDEFINITION" in conan_global_flags
-    assert "OTHER_CFLAGS = $(inherited) flag2" in conan_global_flags
-    assert "OTHER_CPLUSPLUSFLAGS = $(inherited) flag1" in conan_global_flags
-    assert "OTHER_LDFLAGS = $(inherited) flag3 flag4" in conan_global_flags
+    assert '#include "conan_global_flags{}.xcconfig"'.format(filename) in conan_global_flags
+    assert '#include "conan_global_flags{}.xcconfig"'.format(debug_filename) in conan_global_flags
     conan_global_file = client.load("conan_config.xcconfig")
     assert '#include "conan_global_flags.xcconfig"' in conan_global_file
 
 
+@pytest.mark.skipif(platform.system() != "Darwin", reason="Only for MacOS")
 def test_flags_generated_if_only_defines():
     # https://github.com/conan-io/conan/issues/16422
     client = TestClient()
     client.save({"conanfile.txt": "[generators]\nXcodeToolchain\n"})
-    client.run("install . -c 'tools.build:defines=[\"MYDEFINITION\"]'")
-    conan_global_flags = client.load("conan_global_flags.xcconfig")
-    assert "GCC_PREPROCESSOR_DEFINITIONS = $(inherited) MYDEFINITION" in conan_global_flags
+    client.run("install . -s build_type=Release -s arch=x86_64 -c 'tools.build:defines=[\"MYDEFINITION\"]'")
+    filename = _get_filename("Release", "x86_64", None)
+    condition = _condition("Release", "x86_64", None)
+
+    conan_global_flags_props = client.load("conan_global_flags{}.xcconfig".format(filename))
+    assert "GCC_PREPROCESSOR_DEFINITIONS{} = $(inherited) MYDEFINITION".format(condition) in conan_global_flags_props
     conan_global_file = client.load("conan_config.xcconfig")
     assert '#include "conan_global_flags.xcconfig"' in conan_global_file