diff --git a/rust/private/rustc.bzl b/rust/private/rustc.bzl
index 68671387d9..cff05b7fb3 100644
--- a/rust/private/rustc.bzl
+++ b/rust/private/rustc.bzl
@@ -1068,8 +1068,7 @@ def construct_arguments(
         ))
 
     # Ensure the sysroot is set for the target platform
-    if toolchain._experimental_toolchain_generated_sysroot:
-        rustc_flags.add(toolchain.sysroot, format = "--sysroot=%s")
+    rustc_flags.add(toolchain.sysroot, format = "--sysroot=%s")
 
     if toolchain._rename_first_party_crates:
         env["RULES_RUST_THIRD_PARTY_DIR"] = toolchain._third_party_dir
diff --git a/rust/settings/BUILD.bazel b/rust/settings/BUILD.bazel
index 91d01ea85e..eb34098d12 100644
--- a/rust/settings/BUILD.bazel
+++ b/rust/settings/BUILD.bazel
@@ -1,7 +1,6 @@
 load("@bazel_skylib//:bzl_library.bzl", "bzl_library")
 load("@bazel_skylib//rules:common_settings.bzl", "bool_flag", "string_flag")
 load("//rust/private:unpretty.bzl", "rust_unpretty_flag")
-load(":incompatible.bzl", "incompatible_flag")
 
 package(default_visibility = ["//visibility:public"])
 
@@ -85,13 +84,6 @@ bool_flag(
     build_setting_default = True,
 )
 
-# A flag to set rustc --sysroot flag to the sysroot generated by rust_toolchain
-incompatible_flag(
-    name = "experimental_toolchain_generated_sysroot",
-    build_setting_default = True,
-    issue = "https://github.com/bazelbuild/rules_rust/issues/2039",
-)
-
 # A flag to control whether to link libstd dynamically.
 bool_flag(
     name = "experimental_link_std_dylib",
diff --git a/rust/toolchain.bzl b/rust/toolchain.bzl
index 1ff73e6c8a..a1091f7853 100644
--- a/rust/toolchain.bzl
+++ b/rust/toolchain.bzl
@@ -18,7 +18,6 @@ load(
     "is_std_dylib",
     "make_static_lib_symlink",
 )
-load("//rust/settings:incompatible.bzl", "IncompatibleFlagInfo")
 
 rust_analyzer_toolchain = _rust_analyzer_toolchain
 rustfmt_toolchain = _rustfmt_toolchain
@@ -697,7 +696,6 @@ def _rust_toolchain_impl(ctx):
         _experimental_use_cc_common_link = _experimental_use_cc_common_link(ctx),
         _experimental_use_global_allocator = experimental_use_global_allocator,
         _experimental_use_coverage_metadata_files = ctx.attr._experimental_use_coverage_metadata_files[BuildSettingInfo].value,
-        _experimental_toolchain_generated_sysroot = ctx.attr._experimental_toolchain_generated_sysroot[IncompatibleFlagInfo].enabled,
         _no_std = no_std,
     )
     return [
@@ -872,13 +870,6 @@ rust_toolchain = rule(
         "_cc_toolchain": attr.label(
             default = Label("@bazel_tools//tools/cpp:current_cc_toolchain"),
         ),
-        "_experimental_toolchain_generated_sysroot": attr.label(
-            default = Label("//rust/settings:experimental_toolchain_generated_sysroot"),
-            doc = (
-                "Label to a boolean build setting that lets the rule knows wheter to set --sysroot to rustc" +
-                "This flag is only relevant when used together with --@rules_rust//rust/settings:experimental_toolchain_generated_sysroot."
-            ),
-        ),
         "_experimental_use_coverage_metadata_files": attr.label(
             default = Label("//rust/settings:experimental_use_coverage_metadata_files"),
         ),
diff --git a/test/toolchain/toolchain_test.bzl b/test/toolchain/toolchain_test.bzl
index b61a35194a..a06d09373c 100644
--- a/test/toolchain/toolchain_test.bzl
+++ b/test/toolchain/toolchain_test.bzl
@@ -81,7 +81,6 @@ toolchain_adds_rustc_flags_lib_test = analysistest.make(
     _toolchain_adds_rustc_flags_lib_impl,
     config_settings = {
         str(Label("//:extra_rustc_flags")): [CONFIG_FLAG],
-        str(Label("//rust/settings:experimental_toolchain_generated_sysroot")): True,
     },
 )
 
@@ -89,7 +88,6 @@ toolchain_adds_rustc_flags_shared_lib_test = analysistest.make(
     _toolchain_adds_rustc_flags_shared_lib_impl,
     config_settings = {
         str(Label("//:extra_rustc_flags")): [CONFIG_FLAG],
-        str(Label("//rust/settings:experimental_toolchain_generated_sysroot")): True,
     },
 )