diff --git a/compiler/rustc_llvm/llvm-wrapper/PassWrapper.cpp b/compiler/rustc_llvm/llvm-wrapper/PassWrapper.cpp
index 97f95ac01e861..7aa4ddea78e1d 100644
--- a/compiler/rustc_llvm/llvm-wrapper/PassWrapper.cpp
+++ b/compiler/rustc_llvm/llvm-wrapper/PassWrapper.cpp
@@ -812,12 +812,12 @@ extern "C" LLVMRustResult LLVMRustOptimize(
   auto ThinLTOBuffer = std::make_unique<LLVMRustThinLTOBuffer>();
   raw_string_ostream ThinLTODataOS(ThinLTOBuffer->data);
   raw_string_ostream ThinLinkDataOS(ThinLTOBuffer->thin_link_data);
+  bool IsLTO = OptStage == LLVMRustOptStage::ThinLTO ||
+               OptStage == LLVMRustOptStage::FatLTO;
   if (!NoPrepopulatePasses) {
     // The pre-link pipelines don't support O0 and require using
     // buildO0DefaultPipeline() instead. At the same time, the LTO pipelines do
     // support O0 and using them is required.
-    bool IsLTO = OptStage == LLVMRustOptStage::ThinLTO ||
-                 OptStage == LLVMRustOptStage::FatLTO;
     if (OptLevel == OptimizationLevel::O0 && !IsLTO) {
       for (const auto &C : PipelineStartEPCallbacks)
         PB.registerPipelineStartEPCallback(C);
@@ -908,7 +908,10 @@ extern "C" LLVMRustResult LLVMRustOptimize(
 
   // now load "-enzyme" pass:
   // With dlopen, ENZYME macro may not be defined, so check EnzymePtr directly
-  if (EnzymePtr) {
+  // In the case of debug builds with multiple codegen units, we might not
+  // have all function definitions available during the early compiler
+  // invocations. We therefore wait for the final lto step to run Enzyme.
+  if (EnzymePtr && IsLTO) {
 
     if (PrintBeforeEnzyme) {
       // Handle the Rust flag `-Zautodiff=PrintModBefore`.
@@ -929,6 +932,7 @@ extern "C" LLVMRustResult LLVMRustOptimize(
       MPM.addPass(PrintModulePass(outs(), Banner, true, false));
     }
   }
+
   if (PrintPasses) {
     // Print all passes from the PM:
     std::string Pipeline;
diff --git a/tests/ui/autodiff/incremental.rs b/tests/ui/autodiff/incremental.rs
index a79059deaa778..00dd632712aba 100644
--- a/tests/ui/autodiff/incremental.rs
+++ b/tests/ui/autodiff/incremental.rs
@@ -1,6 +1,6 @@
 //@ revisions: DEBUG RELEASE
 //@[RELEASE] compile-flags: -Zautodiff=Enable,NoTT -C opt-level=3 -Clto=fat
-//@[DEBUG]   compile-flags: -Zautodiff=Enable,NoTT -C opt-level=0 -Clto=fat -C debuginfo=2
+//@[DEBUG] compile-flags: -Zautodiff=Enable,NoTT -Copt-level=0 -Clto=fat -Cdebuginfo=2 -Ccodegen-units=8
 //@ needs-enzyme
 //@ incremental
 //@ no-prefer-dynamic
@@ -13,6 +13,10 @@
 // dropped. We now use globals instead and add this test to verify that incremental
 // keeps working. Also testing debug mode while at it.
 
+// We extended this test to use 8 codegen-units in debug mode and call an intrinsic like powi,
+// rather than just simple arithmetic. This caused a compilation failure, since the definition of
+// the intrinsic was not available in the same cgu as the function being differentiated.
+
 use std::autodiff::autodiff_reverse;
 
 #[autodiff_reverse(bar, Duplicated, Duplicated)]
@@ -20,7 +24,7 @@ pub fn foo(r: &[f64; 10], res: &mut f64) {
     let mut output = [0.0; 10];
     output[0] = r[0];
     output[1] = r[1] * r[2];
-    output[2] = r[4] * r[5];
+    output[2] = r[4] * r[5].powi(2);
     output[3] = r[2] * r[6];
     output[4] = r[1] * r[7];
     output[5] = r[2] * r[8];