diff --git a/llvm/test/tools/llvm-objcopy/ELF/add-section-and-set-flags.test b/llvm/test/tools/llvm-objcopy/ELF/add-section-and-set-flags.test
new file mode 100644
--- /dev/null
+++ b/llvm/test/tools/llvm-objcopy/ELF/add-section-and-set-flags.test
@@ -0,0 +1,20 @@
+## Check --set-section-flags works with sections added by --add-section.
+
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy --add-section=foo=/dev/null --set-section-flags=foo=alloc,exclude %t %t.out
+# RUN: llvm-readobj -S %t.out | FileCheck %s
+
+# CHECK:      Name: foo
+# CHECK-NEXT: Type: SHT_PROGBITS
+# CHECK-NEXT: Flags [
+# CHECK-NEXT:   SHF_ALLOC
+# CHECK-NEXT:   SHF_EXCLUDE
+# CHECK-NEXT:   SHF_WRITE
+# CHECK-NEXT: ]
+
+!ELF
+FileHeader:
+  Class:   ELFCLASS64
+  Data:    ELFDATA2LSB
+  Type:    ET_EXEC
+  Machine: EM_X86_64
diff --git a/llvm/tools/llvm-objcopy/ELF/ELFObjcopy.cpp b/llvm/tools/llvm-objcopy/ELF/ELFObjcopy.cpp
--- a/llvm/tools/llvm-objcopy/ELF/ELFObjcopy.cpp
+++ b/llvm/tools/llvm-objcopy/ELF/ELFObjcopy.cpp
@@ -719,16 +719,6 @@
     }
   }
 
-  if (!Config.SetSectionFlags.empty()) {
-    for (auto &Sec : Obj.sections()) {
-      const auto Iter = Config.SetSectionFlags.find(Sec.Name);
-      if (Iter != Config.SetSectionFlags.end()) {
-        const SectionFlagsUpdate &SFU = Iter->second;
-        setSectionFlagsAndType(Sec, SFU.NewFlags);
-      }
-    }
-  }
-
   if (Config.OnlyKeepDebug)
     for (auto &Sec : Obj.sections())
       if (Sec.Flags & SHF_ALLOC && Sec.Type != SHT_NOTE)
@@ -752,6 +742,17 @@
       NewSection.Type = SHT_NOTE;
   }
 
+  // --set-section-flags works with sections added by --add-section.
+  if (!Config.SetSectionFlags.empty()) {
+    for (auto &Sec : Obj.sections()) {
+      const auto Iter = Config.SetSectionFlags.find(Sec.Name);
+      if (Iter != Config.SetSectionFlags.end()) {
+        const SectionFlagsUpdate &SFU = Iter->second;
+        setSectionFlagsAndType(Sec, SFU.NewFlags);
+      }
+    }
+  }
+
   if (!Config.AddGnuDebugLink.empty())
     Obj.addSection<GnuDebugLinkSection>(Config.AddGnuDebugLink,
                                         Config.GnuDebugLinkCRC32);