diff --git a/cabal-testsuite/PackageTests/NewFreeze/cabal.project b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/cabal.project
similarity index 100%
rename from cabal-testsuite/PackageTests/NewFreeze/cabal.project
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/cabal.project
diff --git a/cabal-testsuite/PackageTests/NewFreeze/my-local-package.cabal b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/my-local-package.cabal
similarity index 100%
rename from cabal-testsuite/PackageTests/NewFreeze/my-local-package.cabal
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/my-local-package.cabal
diff --git a/cabal-testsuite/PackageTests/NewFreeze/new_freeze.out b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/new_freeze.out
similarity index 71%
rename from cabal-testsuite/PackageTests/NewFreeze/new_freeze.out
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/new_freeze.out
index fda50e4c6e5..a0d0f0128b3 100644
--- a/cabal-testsuite/PackageTests/NewFreeze/new_freeze.out
+++ b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/new_freeze.out
@@ -19,11 +19,3 @@ In order, the following would be built:
  - my-build-tool-dep-2.0 (exe:my-build-tool) (requires download & build)
  - my-library-dep-1.0 (lib) (requires download & build)
  - my-local-package-1.0 (lib) (first run)
-# cabal new-build
-Resolving dependencies...
-Build profile: -w ghc-<GHCVER> -O1
-In order, the following would be built:
- - my-build-tool-dep-1.0 (exe:my-build-tool) (requires download & build)
- - my-build-tool-dep-3.0 (exe:my-build-tool) (requires download & build)
- - my-library-dep-1.0 (lib) (requires download & build)
- - my-local-package-1.0 (lib) (first run)
diff --git a/cabal-testsuite/PackageTests/NewFreeze/new_freeze.test.hs b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/new_freeze.test.hs
similarity index 90%
rename from cabal-testsuite/PackageTests/NewFreeze/new_freeze.test.hs
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/new_freeze.test.hs
index 1b74c27f5d3..6ff13457481 100644
--- a/cabal-testsuite/PackageTests/NewFreeze/new_freeze.test.hs
+++ b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/new_freeze.test.hs
@@ -34,11 +34,6 @@ main = cabalTest $ withSourceCopy $ do
     -- cabal should be able to find an install plan that fits the constraints
     -- from the freeze file.
     cabal' "new-build" ["--dry-run"] >>= assertDoesNotUseLatestBuildTool
-
-    -- cabal should choose the latest version again after the freeze file is
-    -- removed.
-    liftIO $ removeFile freezeFile
-    cabal' "new-build" ["--dry-run"] >>= assertUsesLatestBuildTool
   where
     assertUsesLatestBuildTool out = do
       assertOutputContains "my-build-tool-dep-3.0 (exe:my-build-tool)" out
diff --git a/cabal-testsuite/PackageTests/NewFreeze/repo/my-build-tool-dep-1.0/my-build-tool-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-build-tool-dep-1.0/my-build-tool-dep.cabal
similarity index 100%
rename from cabal-testsuite/PackageTests/NewFreeze/repo/my-build-tool-dep-1.0/my-build-tool-dep.cabal
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-build-tool-dep-1.0/my-build-tool-dep.cabal
diff --git a/cabal-testsuite/PackageTests/NewFreeze/repo/my-build-tool-dep-2.0/my-build-tool-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-build-tool-dep-2.0/my-build-tool-dep.cabal
similarity index 100%
rename from cabal-testsuite/PackageTests/NewFreeze/repo/my-build-tool-dep-2.0/my-build-tool-dep.cabal
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-build-tool-dep-2.0/my-build-tool-dep.cabal
diff --git a/cabal-testsuite/PackageTests/NewFreeze/repo/my-build-tool-dep-3.0/my-build-tool-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-build-tool-dep-3.0/my-build-tool-dep.cabal
similarity index 100%
rename from cabal-testsuite/PackageTests/NewFreeze/repo/my-build-tool-dep-3.0/my-build-tool-dep.cabal
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-build-tool-dep-3.0/my-build-tool-dep.cabal
diff --git a/cabal-testsuite/PackageTests/NewFreeze/repo/my-library-dep-1.0/my-library-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-library-dep-1.0/my-library-dep.cabal
similarity index 100%
rename from cabal-testsuite/PackageTests/NewFreeze/repo/my-library-dep-1.0/my-library-dep.cabal
rename to cabal-testsuite/PackageTests/NewFreeze/BuildTools/repo/my-library-dep-1.0/my-library-dep.cabal
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/cabal.project b/cabal-testsuite/PackageTests/NewFreeze/Flags/cabal.project
new file mode 100644
index 00000000000..e6fdbadb439
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/cabal.project
@@ -0,0 +1 @@
+packages: .
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/my-local-package.cabal b/cabal-testsuite/PackageTests/NewFreeze/Flags/my-local-package.cabal
new file mode 100644
index 00000000000..ef169c981bd
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/my-local-package.cabal
@@ -0,0 +1,7 @@
+name: my-local-package
+version: 1.0
+cabal-version: 1.20
+build-type: Simple
+
+library
+  build-depends: my-library-dep
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/new_freeze.out b/cabal-testsuite/PackageTests/NewFreeze/Flags/new_freeze.out
new file mode 100644
index 00000000000..b2964507d7e
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/new_freeze.out
@@ -0,0 +1,19 @@
+# cabal update
+Downloading the latest package list from test-local-repo
+# cabal new-build
+Resolving dependencies...
+Build profile: -w ghc-<GHCVER> -O1
+In order, the following would be built:
+ - true-dep-1.0 (lib) (requires download & build)
+ - my-library-dep-1.0 (lib) (requires download & build)
+ - my-local-package-1.0 (lib) (first run)
+# cabal new-freeze
+Resolving dependencies...
+Wrote freeze file: <ROOT>/new_freeze.dist/source/cabal.project.freeze
+# cabal new-build
+Resolving dependencies...
+Build profile: -w ghc-<GHCVER> -O1
+In order, the following would be built:
+ - false-dep-1.0 (lib) (requires download & build)
+ - my-library-dep-1.0 (lib) (requires download & build)
+ - my-local-package-1.0 (lib) (first run)
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/new_freeze.test.hs b/cabal-testsuite/PackageTests/NewFreeze/Flags/new_freeze.test.hs
new file mode 100644
index 00000000000..1a1aa6d283a
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/new_freeze.test.hs
@@ -0,0 +1,35 @@
+import Test.Cabal.Prelude
+import Control.Monad.IO.Class
+import Data.Char
+import System.Directory
+
+-- Test that 'cabal new-freeze' freezes flag choices. my-local-package depends
+-- on my-library-dep. my-library-dep has a flag, my-flag, which defaults to
+-- true.
+main = cabalTest $ withSourceCopy $
+  withRepo "repo" $ do
+    cabal' "new-build" ["--dry-run"] >>= assertDependencyFlagChoice True
+
+    cabal "new-freeze" ["--constraint=my-library-dep -my-flag"]
+
+    cwd <- fmap testCurrentDir getTestEnv
+    let freezeFile = cwd </> "cabal.project.freeze"
+
+    -- The freeze file should constrain the version and the flag.
+    -- TODO: The flag constraint should be qualified. See
+    -- https://github.com/haskell/cabal/issues/5134.
+    assertFileDoesContain freezeFile "any.my-library-dep ==1.0"
+    assertFileDoesContain freezeFile "my-library-dep -my-flag"
+
+    -- cabal should be able to find an install plan that fits the constraints
+    -- from the freeze file.
+    cabal' "new-build" ["--dry-run"] >>= assertDependencyFlagChoice False
+  where
+    -- my-library-dep's flag controls whether it depends on true-dep or
+    -- false-dep, so this function uses the dependency to infer the flag choice.
+    assertDependencyFlagChoice True out = do
+        assertOutputContains "true-dep-1.0 (lib)" out
+        assertOutputDoesNotContain "false-dep" out
+    assertDependencyFlagChoice False out = do
+        assertOutputContains "false-dep-1.0 (lib)" out
+        assertOutputDoesNotContain "true-dep" out
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/false-dep-1.0/false-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/false-dep-1.0/false-dep.cabal
new file mode 100644
index 00000000000..1a2b287f839
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/false-dep-1.0/false-dep.cabal
@@ -0,0 +1,6 @@
+name: false-dep
+version: 1.0
+cabal-version: 1.20
+build-type: Simple
+
+library
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/my-library-dep-1.0/my-library-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/my-library-dep-1.0/my-library-dep.cabal
new file mode 100644
index 00000000000..7a4d72274be
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/my-library-dep-1.0/my-library-dep.cabal
@@ -0,0 +1,15 @@
+name: my-library-dep
+version: 1.0
+cabal-version: 1.20
+build-type: Simple
+
+flag my-flag
+  default: True
+  manual: False
+
+library
+  build-depends: base
+  if flag(my-flag)
+    build-depends: true-dep
+  else
+    build-depends: false-dep
diff --git a/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/true-dep-1.0/true-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/true-dep-1.0/true-dep.cabal
new file mode 100644
index 00000000000..cf9bd7da0b8
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/Flags/repo/true-dep-1.0/true-dep.cabal
@@ -0,0 +1,6 @@
+name: true-dep
+version: 1.0
+cabal-version: 1.20
+build-type: Simple
+
+library
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/Main.hs b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/Main.hs
new file mode 100644
index 00000000000..1a1b44262d6
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/Main.hs
@@ -0,0 +1,3 @@
+import MyLibModule (message)
+
+main = putStrLn message
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/cabal.project b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/cabal.project
new file mode 100644
index 00000000000..e6fdbadb439
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/cabal.project
@@ -0,0 +1 @@
+packages: .
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/my-local-package.cabal b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/my-local-package.cabal
new file mode 100644
index 00000000000..ba8c3562296
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/my-local-package.cabal
@@ -0,0 +1,10 @@
+name: my-local-package
+version: 1.0
+cabal-version: 1.20
+build-type: Simple
+
+executable my-exe
+  hs-source-dirs: .
+  main-is: Main.hs
+  build-depends: base, my-library-dep
+  default-language: Haskell2010
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/new_freeze.out b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/new_freeze.out
new file mode 100644
index 00000000000..52d3b30d236
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/new_freeze.out
@@ -0,0 +1,34 @@
+# cabal update
+Downloading the latest package list from test-local-repo
+# cabal new-build
+Resolving dependencies...
+Build profile: -w ghc-<GHCVER> -O1
+In order, the following would be built:
+ - my-library-dep-2.0 (lib) (requires download & build)
+ - my-local-package-1.0 (exe:my-exe) (first run)
+# cabal new-freeze
+Resolving dependencies...
+Wrote freeze file: <ROOT>/new_freeze.dist/source/cabal.project.freeze
+# cabal new-build
+Resolving dependencies...
+Build profile: -w ghc-<GHCVER> -O1
+In order, the following will be built:
+ - my-library-dep-1.0 (lib) (requires download & build)
+ - my-local-package-1.0 (exe:my-exe) (first run)
+Configuring library for my-library-dep-1.0..
+Preprocessing library for my-library-dep-1.0..
+Building library for my-library-dep-1.0..
+Installing library in <PATH>
+Configuring executable 'my-exe' for my-local-package-1.0..
+Preprocessing executable 'my-exe' for my-local-package-1.0..
+Building executable 'my-exe' for my-local-package-1.0..
+# cabal new-freeze
+Wrote freeze file: <ROOT>/new_freeze.dist/source/cabal.project.freeze
+# cabal new-build
+Resolving dependencies...
+Build profile: -w ghc-<GHCVER> -O1
+In order, the following would be built:
+ - my-library-dep-2.0 (lib) (requires download & build)
+ - my-local-package-1.0 (exe:my-exe) (configuration changed)
+# cabal new-freeze
+Wrote freeze file: <ROOT>/new_freeze.dist/source/cabal.project.freeze
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/new_freeze.test.hs b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/new_freeze.test.hs
new file mode 100644
index 00000000000..de914a226a2
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/new_freeze.test.hs
@@ -0,0 +1,52 @@
+import Test.Cabal.Prelude
+import Control.Monad.IO.Class
+import Data.Char
+import System.Directory
+
+-- Test for 'cabal new-freeze' with only a single library dependency.
+-- my-local-package depends on my-library-dep, which has versions 1.0 and 2.0.
+main = cabalTest $ withSourceCopy $
+  withRepo "repo" $ do
+    cwd <- fmap testCurrentDir getTestEnv
+    let freezeFile = cwd </> "cabal.project.freeze"
+
+    shouldNotExist freezeFile
+
+    -- new-build should choose the latest version for the dependency.
+    cabal' "new-build" ["--dry-run"] >>= assertUsesLatestDependency
+
+    -- Freeze a dependency on the older version.
+    cabal "new-freeze" ["--constraint=my-library-dep==1.0"]
+
+    -- The file should constrain the dependency, but not the local package.
+    shouldExist freezeFile
+    assertFileDoesContain freezeFile "any.my-library-dep ==1.0"
+    assertFileDoesNotContain freezeFile "my-local-package"
+
+    -- cabal should be able to build the package using the constraint from the
+    -- freeze file.
+    cabal' "new-build" [] >>= assertDoesNotUseLatestDependency
+
+    -- Re-running new-freeze should not change the constraints, because cabal
+    -- should use the existing freeze file when choosing the new install plan.
+    cabal "new-freeze" []
+    assertFileDoesContain freezeFile "any.my-library-dep ==1.0"
+
+    -- cabal should choose the latest version again after the freeze file is
+    -- removed.
+    liftIO $ removeFile freezeFile
+    cabal' "new-build" ["--dry-run"] >>= assertUsesLatestDependency
+
+    -- Re-running new-freeze with no constraints or freeze file should constrain
+    -- the dependency to the latest version.
+    cabal "new-freeze" []
+    assertFileDoesContain freezeFile "any.my-library-dep ==2.0"
+    assertFileDoesNotContain freezeFile "my-local-package"
+  where
+    assertUsesLatestDependency out = do
+      assertOutputContains "my-library-dep-2.0 (lib)" out
+      assertOutputDoesNotContain "my-library-dep-1.0" out
+
+    assertDoesNotUseLatestDependency out = do
+      assertOutputContains "my-library-dep-1.0 (lib)" out
+      assertOutputDoesNotContain "my-library-dep-2.0" out
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-1.0/MyLibModule.hs b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-1.0/MyLibModule.hs
new file mode 100644
index 00000000000..10c6c8f7154
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-1.0/MyLibModule.hs
@@ -0,0 +1,3 @@
+module MyLibModule (message) where
+
+message = "Hello"
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-1.0/my-library-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-1.0/my-library-dep.cabal
new file mode 100644
index 00000000000..54b5506b4c4
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-1.0/my-library-dep.cabal
@@ -0,0 +1,10 @@
+name: my-library-dep
+version: 1.0
+cabal-version: 1.20
+build-type: Simple
+
+library
+  hs-source-dirs: .
+  build-depends: base
+  default-language: Haskell2010
+  exposed-modules: MyLibModule
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-2.0/MyLibModule.hs b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-2.0/MyLibModule.hs
new file mode 100644
index 00000000000..10c6c8f7154
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-2.0/MyLibModule.hs
@@ -0,0 +1,3 @@
+module MyLibModule (message) where
+
+message = "Hello"
diff --git a/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-2.0/my-library-dep.cabal b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-2.0/my-library-dep.cabal
new file mode 100644
index 00000000000..98d2146a4ec
--- /dev/null
+++ b/cabal-testsuite/PackageTests/NewFreeze/FreezeFile/repo/my-library-dep-2.0/my-library-dep.cabal
@@ -0,0 +1,10 @@
+name: my-library-dep
+version: 2.0
+cabal-version: 1.20
+build-type: Simple
+
+library
+  hs-source-dirs: .
+  build-depends: base
+  default-language: Haskell2010
+  exposed-modules: MyLibModule