diff --git a/clang-tools-extra/clangd/CompileCommands.cpp b/clang-tools-extra/clangd/CompileCommands.cpp
--- a/clang-tools-extra/clangd/CompileCommands.cpp
+++ b/clang-tools-extra/clangd/CompileCommands.cpp
@@ -9,11 +9,14 @@
 #include "CompileCommands.h"
 #include "Config.h"
 #include "support/Logger.h"
+#include "support/Trace.h"
 #include "clang/Driver/Options.h"
 #include "clang/Frontend/CompilerInvocation.h"
 #include "clang/Tooling/ArgumentsAdjusters.h"
 #include "llvm/ADT/STLExtras.h"
+#include "llvm/ADT/SmallVector.h"
 #include "llvm/ADT/StringRef.h"
+#include "llvm/Option/ArgList.h"
 #include "llvm/Option/Option.h"
 #include "llvm/Support/Allocator.h"
 #include "llvm/Support/Debug.h"
@@ -188,11 +191,33 @@
   return Result;
 }
 
-CommandMangler CommandMangler::forTests() {
-  return CommandMangler();
-}
+CommandMangler CommandMangler::forTests() { return CommandMangler(); }
 
 void CommandMangler::adjust(std::vector<std::string> &Cmd) const {
+  trace::Span S("AdjustCompileFlags");
+  auto &OptTable = clang::driver::getDriverOptTable();
+  // OriginalArgs needs to outlive ArgList.
+  llvm::SmallVector<const char *, 16> OriginalArgs;
+  OriginalArgs.reserve(Cmd.size());
+  for (const std::string &S : Cmd)
+    OriginalArgs.push_back(S.c_str());
+  // ParseArgs propagates missig arg/opt counts on error, but preserves
+  // everything it could parse in ArgList. So we just ignore those counts.
+  unsigned IgnoredCount;
+  auto ArgList = OptTable.ParseArgs(OriginalArgs, IgnoredCount, IgnoredCount);
+
+  // Move the inputs to the end, separated via `--` from flags. This ensures
+  // modifications done in the following steps apply in more cases (like setting
+  // -x, which only affects inputs that come after it).
+  if (!ArgList.hasArgNoClaim(driver::options::OPT__DASH_DASH)) {
+    // In theory there might be more than one input, but clangd can't deal with
+    // them anyway.
+    if (auto *Input = ArgList.getLastArg(driver::options::OPT_INPUT)) {
+      Cmd.insert(Cmd.end(), {"--", Input->getAsString(ArgList)});
+      Cmd.erase(Cmd.begin() + Input->getIndex());
+    }
+  }
+
   for (auto &Edit : Config::current().CompileFlags.Edits)
     Edit(Cmd);
 
@@ -215,7 +240,7 @@
 
   // Don't set `-isysroot` if it is already set or if `--sysroot` is set.
   // `--sysroot` is a superset of the `-isysroot` argument.
-  if (Sysroot && !Has("-isysroot") && !Has("--sysroot")) {
+  if (Sysroot && !Has("--sysroot") && !Has("-isysroot")) {
     ToAppend.push_back("-isysroot");
     ToAppend.push_back(*Sysroot);
   }
diff --git a/clang-tools-extra/clangd/test/did-change-configuration-params.test b/clang-tools-extra/clangd/test/did-change-configuration-params.test
--- a/clang-tools-extra/clangd/test/did-change-configuration-params.test
+++ b/clang-tools-extra/clangd/test/did-change-configuration-params.test
@@ -48,7 +48,7 @@
 #
 # ERR: ASTWorker building file {{.*}}foo.c version 0 with command
 # ERR: [{{.*}}clangd-test2]
-# ERR: clang -c foo.c -Wall -Werror
+# ERR: clang -c -Wall -Werror {{.*}} -- foo.c
 ---
 {"jsonrpc":"2.0","id":5,"method":"shutdown"}
 ---
diff --git a/clang-tools-extra/clangd/unittests/BackgroundIndexTests.cpp b/clang-tools-extra/clangd/unittests/BackgroundIndexTests.cpp
--- a/clang-tools-extra/clangd/unittests/BackgroundIndexTests.cpp
+++ b/clang-tools-extra/clangd/unittests/BackgroundIndexTests.cpp
@@ -133,8 +133,9 @@
   Opts.ContextProvider = [](PathRef P) {
     Config C;
     if (P.endswith("foo.cpp"))
-      C.CompileFlags.Edits.push_back(
-          [](std::vector<std::string> &Argv) { Argv.push_back("-Done=two"); });
+      C.CompileFlags.Edits.push_back([](std::vector<std::string> &Argv) {
+        Argv = tooling::getInsertArgumentAdjuster("-Done=two")(Argv, "");
+      });
     if (P.endswith("baz.cpp"))
       C.Index.Background = Config::BackgroundPolicy::Skip;
     return Context::current().derive(Config::Key, std::move(C));
diff --git a/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp b/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp
--- a/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp
+++ b/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp
@@ -11,6 +11,7 @@
 #include "TestFS.h"
 #include "support/Context.h"
 
+#include "clang/Tooling/ArgumentsAdjusters.h"
 #include "llvm/ADT/ScopeExit.h"
 #include "llvm/ADT/StringExtras.h"
 #include "llvm/Support/FileSystem.h"
@@ -165,13 +166,15 @@
         for (char &C : Arg)
           C = llvm::toUpper(C);
     });
-    Cfg.CompileFlags.Edits.push_back(
-        [](std::vector<std::string> &Argv) { Argv.push_back("--hello"); });
+    Cfg.CompileFlags.Edits.push_back([](std::vector<std::string> &Argv) {
+      Argv = tooling::getInsertArgumentAdjuster("--hello")(Argv, "");
+    });
     WithContextValue WithConfig(Config::Key, std::move(Cfg));
     Mangler.adjust(Cmd);
   }
-  // Edits are applied in given order and before other mangling.
-  EXPECT_THAT(Cmd, ElementsAre(_, "FOO.CC", "--hello"));
+  // Edits are applied in given order and before other mangling and they always
+  // go before filename.
+  EXPECT_THAT(Cmd, ElementsAre(_, "--hello", "--", "FOO.CC"));
 }
 
 static std::string strip(llvm::StringRef Arg, llvm::StringRef Argv) {
@@ -335,9 +338,8 @@
 }
 
 TEST(PrintArgvTest, All) {
-  std::vector<llvm::StringRef> Args = {
-      "one", "two", "thr ee", "f\"o\"ur", "fi\\ve", "$"
-  };
+  std::vector<llvm::StringRef> Args = {"one",      "two",    "thr ee",
+                                       "f\"o\"ur", "fi\\ve", "$"};
   const char *Expected = R"(one two "thr ee" "f\"o\"ur" "fi\\ve" $)";
   EXPECT_EQ(Expected, printArgv(Args));
 }