diff --git a/clang/include/clang/Basic/CodeGenOptions.h b/clang/include/clang/Basic/CodeGenOptions.h
--- a/clang/include/clang/Basic/CodeGenOptions.h
+++ b/clang/include/clang/Basic/CodeGenOptions.h
@@ -207,7 +207,9 @@
   std::string RecordCommandLine;
 
   llvm::SmallVector<std::pair<std::string, std::string>, 0> DebugPrefixMap;
-  std::map<std::string, std::string> CoveragePrefixMap;
+
+  /// Prefix replacement map for source-based code coverage.
+  llvm::SmallVector<std::pair<std::string, std::string>, 0> CoveragePrefixMap;
 
   /// The ABI to use for passing floating point arguments.
   std::string FloatABI;
diff --git a/clang/lib/CodeGen/CoverageMappingGen.cpp b/clang/lib/CodeGen/CoverageMappingGen.cpp
--- a/clang/lib/CodeGen/CoverageMappingGen.cpp
+++ b/clang/lib/CodeGen/CoverageMappingGen.cpp
@@ -1648,8 +1648,12 @@
 std::string CoverageMappingModuleGen::normalizeFilename(StringRef Filename) {
   llvm::SmallString<256> Path(Filename);
   llvm::sys::path::remove_dots(Path, /*remove_dot_dot=*/true);
-  for (const auto &Entry : CGM.getCodeGenOpts().CoveragePrefixMap) {
-    if (llvm::sys::path::replace_path_prefix(Path, Entry.first, Entry.second))
+
+  // Traverse coverage prefix replacement mapping options that are provided in
+  // reverse order to apply them.
+  for (const auto &[From, To] :
+       llvm::reverse(CGM.getCodeGenOpts().CoveragePrefixMap)) {
+    if (llvm::sys::path::replace_path_prefix(Path, From, To))
       break;
   }
   return Path.str().str();
diff --git a/clang/lib/Frontend/CompilerInvocation.cpp b/clang/lib/Frontend/CompilerInvocation.cpp
--- a/clang/lib/Frontend/CompilerInvocation.cpp
+++ b/clang/lib/Frontend/CompilerInvocation.cpp
@@ -1701,8 +1701,7 @@
 
   for (const auto &Arg : Args.getAllArgValues(OPT_fcoverage_prefix_map_EQ)) {
     auto Split = StringRef(Arg).split('=');
-    Opts.CoveragePrefixMap.insert(
-        {std::string(Split.first), std::string(Split.second)});
+    Opts.CoveragePrefixMap.emplace_back(Split.first, Split.second);
   }
 
   const llvm::Triple::ArchType DebugEntryValueArchs[] = {
diff --git a/clang/test/Profile/coverage-prefix-map.c b/clang/test/Profile/coverage-prefix-map.c
--- a/clang/test/Profile/coverage-prefix-map.c
+++ b/clang/test/Profile/coverage-prefix-map.c
@@ -19,3 +19,13 @@
 
 // RUN: %clang_cc1 -fprofile-instrument=clang -fcoverage-mapping -emit-llvm -mllvm -enable-name-compression=false -main-file-name coverage-prefix-map.c %t/root/nested/coverage-prefix-map.c -fcoverage-compilation-dir=/custom -fcoverage-prefix-map=/custom=/nonsense -o - | FileCheck --check-prefix=COVERAGE-COMPILATION-DIR %s
 // COVERAGE-COMPILATION-DIR: @__llvm_coverage_mapping = {{.*"\\02.*}}nonsense
+
+// Test that last -fcoverage-prefix-map option (-fcoverage-prefix-map==newpath) is applied.
+// RUN: %clang_cc1 -fprofile-instrument=clang -fcoverage-mapping -emit-llvm -mllvm -enable-name-compression=false -main-file-name coverage-prefix-map.c %t/root/nested/coverage-prefix-map.c -fcoverage-prefix-map=%/t/root=. -fcoverage-prefix-map==newpath -o - | FileCheck --check-prefix=COVERAGE-PREFIX-MAP-ORDER %s
+// COVERAGE-PREFIX-MAP-ORDER: @__llvm_coverage_mapping = {{.*"\\02.*newpath.*root.*nested.*coverage-prefix-map\.c}}
+
+// Test that last -fcoverage-prefix-map option (-fcoverage-prefix-map=%/t/root=.) is applied.
+// RUN: %clang_cc1 -fprofile-instrument=clang -fcoverage-mapping -emit-llvm -mllvm -enable-name-compression=false -main-file-name coverage-prefix-map.c %t/root/nested/coverage-prefix-map.c -fcoverage-prefix-map==newpath -fcoverage-prefix-map=%/t/root=. -o - | FileCheck --check-prefix=COVERAGE-PREFIX-MAP-REORDER %s
+// COVERAGE-PREFIX-MAP-REORDER: @__llvm_coverage_mapping =
+// COVERAGE-PREFIX-MAP-REORDER-NOT: newpath
+// COVERAGE-PREFIX-MAP-REORDER-SAME: nested{{.*coverage-prefix-map\.c}}