diff --git a/cargo/private/cargo_build_script.bzl b/cargo/private/cargo_build_script.bzl
index b1c630a86e..0e8dc8d49a 100644
--- a/cargo/private/cargo_build_script.bzl
+++ b/cargo/private/cargo_build_script.bzl
@@ -528,6 +528,8 @@ def _cargo_build_script_impl(ctx):
     env["CARGO_ENCODED_RUSTFLAGS"] = "\\x1f".join([
         # Allow build scripts to locate the generated sysroot
         "--sysroot=${{pwd}}/{}".format(toolchain.sysroot),
+        # Keep build scripts from baking the exec root into their output
+        "--remap-path-prefix=${pwd}=.",
     ] + ctx.attr.rustc_flags)
 
     for f in ctx.attr.crate_features:
diff --git a/cargo/tests/cargo_build_script/tools_exec/build.rs b/cargo/tests/cargo_build_script/tools_exec/build.rs
index 397281bd57..230bc5b190 100644
--- a/cargo/tests/cargo_build_script/tools_exec/build.rs
+++ b/cargo/tests/cargo_build_script/tools_exec/build.rs
@@ -8,14 +8,17 @@ fn test_encoded_rustflags() {
         .split('\x1f')
         .map(str::to_string)
         .collect();
-    assert_eq!(flags.len(), 2);
+    assert_eq!(flags.len(), 3);
 
     assert!(flags[0].starts_with("--sysroot"));
 
     // Ensure the `pwd` template has been resolved
     assert!(!flags[0].contains("${pwd}"));
 
-    assert_eq!(flags[1], "--cfg=foo=\"bar\"");
+    assert!(flags[1].starts_with("--remap-path-prefix"));
+    assert!(!flags[1].contains("${pwd}"));
+
+    assert_eq!(flags[2], "--cfg=foo=\"bar\"");
 }
 
 /// Ensure Make variables provided by the `toolchains` attribute are expandable.