diff --git a/src/bootstrap/config.rs b/src/bootstrap/config.rs
index 133a66ff5cdf4..94a48a79b0939 100644
--- a/src/bootstrap/config.rs
+++ b/src/bootstrap/config.rs
@@ -1228,7 +1228,10 @@ impl Config {
                 if let Some(ref s) = cfg.llvm_config {
                     target.llvm_config = Some(config.src.join(s));
                 }
-                target.llvm_has_rust_patches = cfg.llvm_has_rust_patches;
+                if let Some(patches) = cfg.llvm_has_rust_patches {
+                    assert!(config.submodules.is_some(), "cannot set `llvm-hash-rust-patches` for a managed submodule");
+                    target.llvm_has_rust_patches = Some(patches);
+                }
                 if let Some(ref s) = cfg.llvm_filecheck {
                     target.llvm_filecheck = Some(config.src.join(s));
                 }