diff --git a/ChangeLog.md b/ChangeLog.md
index 1b194fddd0..62aa88ad3d 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -42,6 +42,8 @@ Bug fixes:
   was tried to be registered. This is now fixed by always building internal
   libraries. See
   [#3996](https://github.com/commercialhaskell/stack/issues/3996).
+* Order of commandline arguments does not matter anymore.
+  See [#3959](https://github.com/commercialhaskell/stack/issues/3959)
 * When prompting users about saving their Hackage credentials on upload,
   flush to stdout before waiting for the response so the prompt actually
   displays.
diff --git a/src/Stack/Options/BenchParser.hs b/src/Stack/Options/BenchParser.hs
index d25c0a90d3..d5b751c4a2 100644
--- a/src/Stack/Options/BenchParser.hs
+++ b/src/Stack/Options/BenchParser.hs
@@ -19,7 +19,7 @@ benchOptsParser hide0 = BenchmarkOptsMonoid
                                  help ("Forward BENCH_ARGS to the benchmark suite. " <>
                                        "Supports templates from `cabal bench`") <>
                                  hide))
-        <*> optionalFirst (switch (long "no-run-benchmarks" <>
+        <*> optionalFirst (flag' True (long "no-run-benchmarks" <>
                           help "Disable running of benchmarks. (Benchmarks will still be built.)" <>
                              hide))
    where hide = hideMods hide0
diff --git a/src/Stack/Options/TestParser.hs b/src/Stack/Options/TestParser.hs
index 08b3b4bf0b..e5c735edd1 100644
--- a/src/Stack/Options/TestParser.hs
+++ b/src/Stack/Options/TestParser.hs
@@ -27,12 +27,12 @@ testOptsParser hide0 =
                          help "Arguments passed in to the test suite program" <>
                          hide)))
         <*> optionalFirst
-                (switch
+                (flag' True
                     (long "coverage" <>
                      help "Generate a code coverage report" <>
                      hide))
         <*> optionalFirst
-                (switch
+                (flag' True
                     (long "no-run-tests" <>
                      help "Disable running of tests. (Tests will still be built.)" <>
                      hide))
diff --git a/test/integration/tests/3959-order-of-flags/Main.hs b/test/integration/tests/3959-order-of-flags/Main.hs
new file mode 100644
index 0000000000..650bf92469
--- /dev/null
+++ b/test/integration/tests/3959-order-of-flags/Main.hs
@@ -0,0 +1,21 @@
+import StackTest
+
+import Control.Monad (unless)
+import Data.List (isInfixOf)
+
+-- Integration test for https://github.com/commercialhaskell/stack/issues/3959
+main :: IO ()
+main = do
+  checkFlagsBeforeCommand
+  checkFlagsAfterCommand
+
+checkFlagsBeforeCommand :: IO ()
+checkFlagsBeforeCommand = stackCheckStderr ["--test", "--no-run-tests", "build"] checker
+
+checkFlagsAfterCommand :: IO ()
+checkFlagsAfterCommand = stackCheckStderr ["build", "--test", "--no-run-tests"] checker
+
+checker :: String -> IO ()
+checker output = do
+  let testsAreDisabled = any (\ln -> "Test running disabled by" `isInfixOf` ln) (lines output)
+  unless testsAreDisabled $ fail "Tests should not be run"
diff --git a/test/integration/tests/3959-order-of-flags/files/package.yaml b/test/integration/tests/3959-order-of-flags/files/package.yaml
new file mode 100644
index 0000000000..43895dbbda
--- /dev/null
+++ b/test/integration/tests/3959-order-of-flags/files/package.yaml
@@ -0,0 +1,10 @@
+name: issue3959
+version: 0.1.0.0
+
+dependencies:
+- base
+
+tests:
+  test:
+    main:                Spec.hs
+    source-dirs:         test
diff --git a/test/integration/tests/3959-order-of-flags/files/stack.yaml b/test/integration/tests/3959-order-of-flags/files/stack.yaml
new file mode 100644
index 0000000000..cee3f00b38
--- /dev/null
+++ b/test/integration/tests/3959-order-of-flags/files/stack.yaml
@@ -0,0 +1 @@
+resolver: lts-11.6
diff --git a/test/integration/tests/3959-order-of-flags/files/test/Spec.hs b/test/integration/tests/3959-order-of-flags/files/test/Spec.hs
new file mode 100644
index 0000000000..6efee5cea7
--- /dev/null
+++ b/test/integration/tests/3959-order-of-flags/files/test/Spec.hs
@@ -0,0 +1,2 @@
+main :: IO ()
+main = fail "this always fails for the test"