diff --git a/clang/lib/CodeGen/BackendUtil.cpp b/clang/lib/CodeGen/BackendUtil.cpp
--- a/clang/lib/CodeGen/BackendUtil.cpp
+++ b/clang/lib/CodeGen/BackendUtil.cpp
@@ -32,6 +32,7 @@
 #include "llvm/IR/LegacyPassManager.h"
 #include "llvm/IR/Module.h"
 #include "llvm/IR/ModuleSummaryIndex.h"
+#include "llvm/IR/PassManager.h"
 #include "llvm/IR/Verifier.h"
 #include "llvm/LTO/LTOBackend.h"
 #include "llvm/MC/MCAsmInfo.h"
@@ -1001,6 +1002,15 @@
                               const Triple &TargetTriple,
                               const LangOptions &LangOpts,
                               const CodeGenOptions &CodeGenOpts) {
+  if (CodeGenOpts.SanitizeCoverageType ||
+      CodeGenOpts.SanitizeCoverageIndirectCalls ||
+      CodeGenOpts.SanitizeCoverageTraceCmp) {
+    auto SancovOpts = getSancovOptsFromCGOpts(CodeGenOpts);
+    MPM.addPass(ModuleSanitizerCoveragePass(
+        SancovOpts, CodeGenOpts.SanitizeCoverageWhitelistFiles,
+        CodeGenOpts.SanitizeCoverageBlacklistFiles));
+  }
+
   auto ASanPass = [&](SanitizerMask Mask, bool CompileKernel) {
     MPM.addPass(RequireAnalysisPass<ASanGlobalsMetadataAnalysis, Module>());
     bool Recover = CodeGenOpts.SanitizeRecover.has(Mask);
@@ -1249,6 +1259,20 @@
             [](FunctionPassManager &FPM, PassBuilder::OptimizationLevel Level) {
               FPM.addPass(BoundsCheckingPass());
             });
+
+      if (CodeGenOpts.SanitizeCoverageType ||
+          CodeGenOpts.SanitizeCoverageIndirectCalls ||
+          CodeGenOpts.SanitizeCoverageTraceCmp) {
+        PB.registerOptimizerLastEPCallback(
+            [this](ModulePassManager &MPM,
+                   PassBuilder::OptimizationLevel Level) {
+              auto SancovOpts = getSancovOptsFromCGOpts(CodeGenOpts);
+              MPM.addPass(ModuleSanitizerCoveragePass(
+                  SancovOpts, CodeGenOpts.SanitizeCoverageWhitelistFiles,
+                  CodeGenOpts.SanitizeCoverageBlacklistFiles));
+            });
+      }
+
       if (LangOpts.Sanitize.has(SanitizerKind::Memory)) {
         int TrackOrigins = CodeGenOpts.SanitizeMemoryTrackOrigins;
         bool Recover = CodeGenOpts.SanitizeRecover.has(SanitizerKind::Memory);
@@ -1257,17 +1281,19 @@
               MPM.addPass(MemorySanitizerPass({TrackOrigins, Recover, false}));
             });
         PB.registerOptimizerLastEPCallback(
-            [TrackOrigins, Recover](FunctionPassManager &FPM,
+            [TrackOrigins, Recover](ModulePassManager &MPM,
                                     PassBuilder::OptimizationLevel Level) {
-              FPM.addPass(MemorySanitizerPass({TrackOrigins, Recover, false}));
+              MPM.addPass(createModuleToFunctionPassAdaptor(
+                  MemorySanitizerPass({TrackOrigins, Recover, false})));
             });
       }
       if (LangOpts.Sanitize.has(SanitizerKind::Thread)) {
         PB.registerPipelineStartEPCallback(
             [](ModulePassManager &MPM) { MPM.addPass(ThreadSanitizerPass()); });
         PB.registerOptimizerLastEPCallback(
-            [](FunctionPassManager &FPM, PassBuilder::OptimizationLevel Level) {
-              FPM.addPass(ThreadSanitizerPass());
+            [](ModulePassManager &MPM, PassBuilder::OptimizationLevel Level) {
+              MPM.addPass(
+                  createModuleToFunctionPassAdaptor(ThreadSanitizerPass()));
             });
       }
       if (LangOpts.Sanitize.has(SanitizerKind::Address)) {
@@ -1278,10 +1304,11 @@
         bool Recover = CodeGenOpts.SanitizeRecover.has(SanitizerKind::Address);
         bool UseAfterScope = CodeGenOpts.SanitizeAddressUseAfterScope;
         PB.registerOptimizerLastEPCallback(
-            [Recover, UseAfterScope](FunctionPassManager &FPM,
+            [Recover, UseAfterScope](ModulePassManager &MPM,
                                      PassBuilder::OptimizationLevel Level) {
-              FPM.addPass(AddressSanitizerPass(
-                  /*CompileKernel=*/false, Recover, UseAfterScope));
+              MPM.addPass(
+                  createModuleToFunctionPassAdaptor(AddressSanitizerPass(
+                      /*CompileKernel=*/false, Recover, UseAfterScope)));
             });
         bool ModuleUseAfterScope = asanUseGlobalsGC(TargetTriple, CodeGenOpts);
         bool UseOdrIndicator = CodeGenOpts.SanitizeAddressUseOdrIndicator;
@@ -1325,15 +1352,6 @@
       }
     }
 
-    if (CodeGenOpts.SanitizeCoverageType ||
-        CodeGenOpts.SanitizeCoverageIndirectCalls ||
-        CodeGenOpts.SanitizeCoverageTraceCmp) {
-      auto SancovOpts = getSancovOptsFromCGOpts(CodeGenOpts);
-      MPM.addPass(ModuleSanitizerCoveragePass(
-          SancovOpts, CodeGenOpts.SanitizeCoverageWhitelistFiles,
-          CodeGenOpts.SanitizeCoverageBlacklistFiles));
-    }
-
     if (LangOpts.Sanitize.has(SanitizerKind::HWAddress)) {
       bool Recover = CodeGenOpts.SanitizeRecover.has(SanitizerKind::HWAddress);
       MPM.addPass(HWAddressSanitizerPass(
diff --git a/clang/test/CodeGen/sancov-new-pm.c b/clang/test/CodeGen/sancov-new-pm.c
--- a/clang/test/CodeGen/sancov-new-pm.c
+++ b/clang/test/CodeGen/sancov-new-pm.c
@@ -1,10 +1,6 @@
 // Test that SanitizerCoverage works under the new pass manager.
 // RUN: %clang -target x86_64-linux-gnu -fsanitize=fuzzer %s -fexperimental-new-pass-manager -S -emit-llvm -o - | FileCheck %s --check-prefixes=CHECK,CHECK-O0
 // RUN: %clang -target x86_64-linux-gnu -fsanitize=fuzzer %s -fexperimental-new-pass-manager -O2 -S -emit-llvm -o - | FileCheck %s --check-prefixes=CHECK,CHECK-O2
-// RUN: %clang -target x86_64-linux-gnu -fsanitize=fuzzer %s -fexperimental-new-pass-manager -flto -S -emit-llvm -o - | FileCheck %s --check-prefixes=CHECK,CHECK-O0
-// RUN: %clang -target x86_64-linux-gnu -fsanitize=fuzzer %s -fexperimental-new-pass-manager -flto -O2 -S -emit-llvm -o - | FileCheck %s --check-prefixes=CHECK,CHECK-O2
-// RUN: %clang -target x86_64-linux-gnu -fsanitize=fuzzer %s -fexperimental-new-pass-manager -flto=thin -S -emit-llvm -o - | FileCheck %s --check-prefixes=CHECK,CHECK-O0
-// RUN: %clang -target x86_64-linux-gnu -fsanitize=fuzzer %s -fexperimental-new-pass-manager -flto=thin -O2 -S -emit-llvm -o - | FileCheck %s --check-prefixes=CHECK,CHECK-O2,CHECK-O2-THINLTO
 
 extern void *memcpy(void *, const void *, unsigned long);
 extern int printf(const char *restrict, ...);
@@ -29,10 +25,10 @@
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_cmp2(i16 zeroext, i16 zeroext)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_cmp4(i32 zeroext, i32 zeroext)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_cmp8(i64, i64)
-// CHECK-O2-THINLTO-NOT: declare void @__sanitizer_cov_trace_const_cmp1(i8 zeroext, i8 zeroext)
+// CHECK-O2-NOT: declare void @__sanitizer_cov_trace_const_cmp1(i8 zeroext, i8 zeroext)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_const_cmp2(i16 zeroext, i16 zeroext)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_const_cmp4(i32 zeroext, i32 zeroext)
-// CHECK-O2-THINLTO-NOT: declare void @__sanitizer_cov_trace_const_cmp8(i64, i64)
+// CHECK-O2-NOT: declare void @__sanitizer_cov_trace_const_cmp8(i64, i64)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_div4(i32 zeroext)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_div8(i64)
 // CHECK-O0-DAG: declare void @__sanitizer_cov_trace_gep(i64)
diff --git a/llvm/include/llvm/Passes/PassBuilder.h b/llvm/include/llvm/Passes/PassBuilder.h
--- a/llvm/include/llvm/Passes/PassBuilder.h
+++ b/llvm/include/llvm/Passes/PassBuilder.h
@@ -600,7 +600,7 @@
   /// is not triggered at O0. Extensions to the O0 pipeline should append their
   /// passes to the end of the overall pipeline.
   void registerOptimizerLastEPCallback(
-      const std::function<void(FunctionPassManager &, OptimizationLevel)> &C) {
+      const std::function<void(ModulePassManager &, OptimizationLevel)> &C) {
     OptimizerLastEPCallbacks.push_back(C);
   }
 
@@ -728,7 +728,7 @@
       CGSCCOptimizerLateEPCallbacks;
   SmallVector<std::function<void(FunctionPassManager &, OptimizationLevel)>, 2>
       VectorizerStartEPCallbacks;
-  SmallVector<std::function<void(FunctionPassManager &, OptimizationLevel)>, 2>
+  SmallVector<std::function<void(ModulePassManager &, OptimizationLevel)>, 2>
       OptimizerLastEPCallbacks;
   // Module callbacks
   SmallVector<std::function<void(ModulePassManager &)>, 2>
diff --git a/llvm/lib/Passes/PassBuilder.cpp b/llvm/lib/Passes/PassBuilder.cpp
--- a/llvm/lib/Passes/PassBuilder.cpp
+++ b/llvm/lib/Passes/PassBuilder.cpp
@@ -1073,12 +1073,12 @@
   if (PTO.Coroutines)
     OptimizePM.addPass(CoroCleanupPass());
 
-  for (auto &C : OptimizerLastEPCallbacks)
-    C(OptimizePM, Level);
-
   // Add the core optimizing pipeline.
   MPM.addPass(createModuleToFunctionPassAdaptor(std::move(OptimizePM)));
 
+  for (auto &C : OptimizerLastEPCallbacks)
+    C(MPM, Level);
+
   if (PTO.CallGraphProfile)
     MPM.addPass(CGProfilePass());
 
diff --git a/llvm/tools/opt/NewPMDriver.cpp b/llvm/tools/opt/NewPMDriver.cpp
--- a/llvm/tools/opt/NewPMDriver.cpp
+++ b/llvm/tools/opt/NewPMDriver.cpp
@@ -194,7 +194,7 @@
         });
   if (tryParsePipelineText<FunctionPassManager>(PB, OptimizerLastEPPipeline))
     PB.registerOptimizerLastEPCallback(
-        [&PB, VerifyEachPass, DebugLogging](FunctionPassManager &PM,
+        [&PB, VerifyEachPass, DebugLogging](ModulePassManager &PM,
                                             PassBuilder::OptimizationLevel) {
           ExitOnError Err("Unable to parse OptimizerLastEP pipeline: ");
           Err(PB.parsePassPipeline(PM, OptimizerLastEPPipeline, VerifyEachPass,