diff --git a/utils/wasm-builder/src/prerequisites.rs b/utils/wasm-builder/src/prerequisites.rs
index 0dad8b781ae5a..c45f7933a1de3 100644
--- a/utils/wasm-builder/src/prerequisites.rs
+++ b/utils/wasm-builder/src/prerequisites.rs
@@ -138,6 +138,13 @@ fn check_wasm_toolchain_installed(
 	build_cmd.env_remove("CARGO_TARGET_DIR");
 	run_cmd.env_remove("CARGO_TARGET_DIR");
 
+	// Make sure the host's flags aren't used here, e.g. if an alternative linker is specified
+	// in the RUSTFLAGS then the check we do here will break unless we clear these.
+	build_cmd.env_remove("CARGO_ENCODED_RUSTFLAGS");
+	run_cmd.env_remove("CARGO_ENCODED_RUSTFLAGS");
+	build_cmd.env_remove("RUSTFLAGS");
+	run_cmd.env_remove("RUSTFLAGS");
+
 	build_cmd.output().map_err(|_| err_msg.clone()).and_then(|s| {
 		if s.status.success() {
 			let version = run_cmd.output().ok().and_then(|o| String::from_utf8(o.stdout).ok());