diff --git a/home-manager/po/home-manager.pot b/home-manager/po/home-manager.pot
index 2fcdc5a6061a..6817fd554502 100644
--- a/home-manager/po/home-manager.pot
+++ b/home-manager/po/home-manager.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Home Manager\n"
 "Report-Msgid-Bugs-To: https://github.com/nix-community/home-manager/issues\n"
-"POT-Creation-Date: 2024-04-17 23:19+0200\n"
+"POT-Creation-Date: 2025-01-03 09:09+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -23,36 +23,36 @@ msgstr ""
 msgid "%s: missing argument for %s"
 msgstr ""
 
-#: home-manager/home-manager:64
+#: home-manager/home-manager:69
 msgid "No configuration file found at %s"
 msgstr ""
 
 #. translators: The first '%s' specifier will be replaced by either
 #. 'home.nix' or 'flake.nix'.
-#: home-manager/home-manager:81 home-manager/home-manager:85
-#: home-manager/home-manager:184
+#: home-manager/home-manager:86 home-manager/home-manager:90
+#: home-manager/home-manager:189
 msgid ""
 "Keeping your Home Manager %s in %s is deprecated,\n"
 "please move it to %s"
 msgstr ""
 
-#: home-manager/home-manager:92
+#: home-manager/home-manager:97
 msgid "No configuration file found. Please create one at %s"
 msgstr ""
 
-#: home-manager/home-manager:107
+#: home-manager/home-manager:112
 msgid "Home Manager not found at %s."
 msgstr ""
 
 #. translators: This message will be seen by very few users that likely are familiar with English. So feel free to leave this untranslated.
-#: home-manager/home-manager:115
+#: home-manager/home-manager:120
 msgid ""
 "The fallback Home Manager path %s has been deprecated and a file/directory "
 "was found there."
 msgstr ""
 
 #. translators: This message will be seen by very few users that likely are familiar with English. So feel free to leave this untranslated.
-#: home-manager/home-manager:118
+#: home-manager/home-manager:123
 msgid ""
 "To remove this warning, do one of the following.\n"
 "\n"
@@ -73,42 +73,42 @@ msgid ""
 "     $ rm -r \"%s\""
 msgstr ""
 
-#: home-manager/home-manager:146
+#: home-manager/home-manager:151
 msgid "Sanity checking Nix"
 msgstr ""
 
-#: home-manager/home-manager:166
+#: home-manager/home-manager:171
 msgid "Could not find suitable profile directory, tried %s and %s"
 msgstr ""
 
 #. translators: Here "flake" is a noun that refers to the Nix Flakes feature.
-#: home-manager/home-manager:221
+#: home-manager/home-manager:226
 msgid "Can't inspect options of a flake configuration"
 msgstr ""
 
-#: home-manager/home-manager:296 home-manager/home-manager:319
-#: home-manager/home-manager:1051
+#: home-manager/home-manager:301 home-manager/home-manager:324
+#: home-manager/home-manager:1061
 msgid "%s: unknown option '%s'"
 msgstr ""
 
-#: home-manager/home-manager:301 home-manager/home-manager:1052
+#: home-manager/home-manager:306 home-manager/home-manager:1062
 msgid "Run '%s --help' for usage help"
 msgstr ""
 
-#: home-manager/home-manager:327 home-manager/home-manager:431
+#: home-manager/home-manager:332 home-manager/home-manager:437
 msgid "The file %s already exists, leaving it unchanged..."
 msgstr ""
 
-#: home-manager/home-manager:329 home-manager/home-manager:433
+#: home-manager/home-manager:334 home-manager/home-manager:439
 msgid "Creating %s..."
 msgstr ""
 
-#: home-manager/home-manager:475
+#: home-manager/home-manager:481
 msgid "Creating initial Home Manager generation..."
 msgstr ""
 
 #. translators: The "%s" specifier will be replaced by a file path.
-#: home-manager/home-manager:480
+#: home-manager/home-manager:486
 msgid ""
 "All done! The home-manager tool should now be installed and you can edit\n"
 "\n"
@@ -119,7 +119,7 @@ msgid ""
 msgstr ""
 
 #. translators: The "%s" specifier will be replaced by a URL.
-#: home-manager/home-manager:485
+#: home-manager/home-manager:491
 msgid ""
 "Uh oh, the installation failed! Please create an issue at\n"
 "\n"
@@ -129,11 +129,11 @@ msgid ""
 msgstr ""
 
 #. translators: Here "flake" is a noun that refers to the Nix Flakes feature.
-#: home-manager/home-manager:496
+#: home-manager/home-manager:502
 msgid "Can't instantiate a flake configuration"
 msgstr ""
 
-#: home-manager/home-manager:572
+#: home-manager/home-manager:578
 msgid ""
 "There is %d unread and relevant news item.\n"
 "Read it by running the command \"%s news\"."
@@ -143,72 +143,72 @@ msgid_plural ""
 msgstr[0] ""
 msgstr[1] ""
 
-#: home-manager/home-manager:586
+#: home-manager/home-manager:592
 msgid "Unknown \"news.display\" setting \"%s\"."
 msgstr ""
 
-#: home-manager/home-manager:594
+#: home-manager/home-manager:600
 #, sh-format
 msgid "Please set the $EDITOR or $VISUAL environment variable"
 msgstr ""
 
-#: home-manager/home-manager:612
+#: home-manager/home-manager:618
 msgid "Cannot run build in read-only directory"
 msgstr ""
 
-#: home-manager/home-manager:693
+#: home-manager/home-manager:699
 msgid "No generation with ID %s"
 msgstr ""
 
-#: home-manager/home-manager:695
+#: home-manager/home-manager:701
 msgid "Cannot remove the current generation %s"
 msgstr ""
 
-#: home-manager/home-manager:697
+#: home-manager/home-manager:703
 msgid "Removing generation %s"
 msgstr ""
 
-#: home-manager/home-manager:718
+#: home-manager/home-manager:724
 msgid "No generations to expire"
 msgstr ""
 
-#: home-manager/home-manager:729
+#: home-manager/home-manager:735
 msgid "No home-manager packages seem to be installed."
 msgstr ""
 
-#: home-manager/home-manager:811
+#: home-manager/home-manager:820
 msgid "Unknown argument %s"
 msgstr ""
 
-#: home-manager/home-manager:835
+#: home-manager/home-manager:845
 msgid "This will remove Home Manager from your system."
 msgstr ""
 
-#: home-manager/home-manager:838
+#: home-manager/home-manager:848
 msgid "This is a dry run, nothing will actually be uninstalled."
 msgstr ""
 
-#: home-manager/home-manager:842
+#: home-manager/home-manager:852
 msgid "Really uninstall Home Manager?"
 msgstr ""
 
-#: home-manager/home-manager:848
+#: home-manager/home-manager:858
 msgid "Switching to empty Home Manager configuration..."
 msgstr ""
 
-#: home-manager/home-manager:863
+#: home-manager/home-manager:873
 msgid "Yay!"
 msgstr ""
 
-#: home-manager/home-manager:868
+#: home-manager/home-manager:878
 msgid "Home Manager is uninstalled but your home.nix is left untouched."
 msgstr ""
 
-#: home-manager/home-manager:1091
+#: home-manager/home-manager:1101
 msgid "expire-generations expects one argument, got %d."
 msgstr ""
 
-#: home-manager/home-manager:1113
+#: home-manager/home-manager:1123
 msgid "Unknown command: %s"
 msgstr ""
 
diff --git a/modules/files.nix b/modules/files.nix
index 59e9c25783c7..8c047bbeb736 100644
--- a/modules/files.nix
+++ b/modules/files.nix
@@ -105,10 +105,7 @@ in
     # 1. Remove files from the old generation that are not in the new
     #    generation.
     #
-    # 2. Switch over the Home Manager gcroot and current profile
-    #    links.
-    #
-    # 3. Symlink files from the new generation into $HOME.
+    # 2. Symlink files from the new generation into $HOME.
     #
     # This order is needed to ensure that we always know which links
     # belong to which generation. Specifically, if we're moving from
@@ -215,28 +212,6 @@ in
           }
 
           cleanOldGen
-
-          if [[ ! -v oldGenPath || "$oldGenPath" != "$newGenPath" ]] ; then
-            _i "Creating profile generation %s" $newGenNum
-            if [[ -e "$genProfilePath"/manifest.json ]] ; then
-              # Remove all packages from "$genProfilePath"
-              # `nix profile remove '.*' --profile "$genProfilePath"` was not working, so here is a workaround:
-              nix profile list --profile "$genProfilePath" \
-                | cut -d ' ' -f 4 \
-                | xargs -rt $DRY_RUN_CMD nix profile remove $VERBOSE_ARG --profile "$genProfilePath"
-              run nix profile install $VERBOSE_ARG --profile "$genProfilePath" "$newGenPath"
-            else
-              run nix-env $VERBOSE_ARG --profile "$genProfilePath" --set "$newGenPath"
-            fi
-
-            run --quiet nix-store --realise "$newGenPath" --add-root "$newGenGcPath" --indirect
-            if [[ -e "$legacyGenGcPath" ]]; then
-              run rm $VERBOSE_ARG "$legacyGenGcPath"
-            fi
-          else
-            _i "No change so reusing latest profile generation %s" "$oldGenNum"
-          fi
-
           linkNewGen
         ''
     );
diff --git a/modules/home-environment.nix b/modules/home-environment.nix
index 2673d1711ad7..fffb3b1cf02d 100644
--- a/modules/home-environment.nix
+++ b/modules/home-environment.nix
@@ -583,9 +583,17 @@ in
 
     home.packages = [ config.home.sessionVariablesPackage ];
 
-    # A dummy entry acting as a boundary between the activation
-    # script's "check" and the "write" phases.
-    home.activation.writeBoundary = hm.dag.entryAnywhere "";
+    # The entry acting as a boundary between the activation script's "check" and
+    # the "write" phases. This is where we commit to attempting to actually
+    # activate the configuration.
+    home.activation.writeBoundary = hm.dag.entryAnywhere ''
+      if [[ ! -v oldGenPath || "$oldGenPath" != "$newGenPath" ]] ; then
+        _i "Creating new profile generation"
+        run nix-env $VERBOSE_ARG --profile "$genProfilePath" --set "$newGenPath"
+      else
+        _i "No change so reusing latest profile generation"
+      fi
+    '';
 
     # Install packages to the user environment.
     #
@@ -718,7 +726,20 @@ in
             checkHomeDirectory ${escapeShellArg config.home.homeDirectory}
           fi
 
+          # Create a temporary GC root to prevent collection during activation.
+          trap 'run rm -f $VERBOSE_ARG "$newGenGcPath"' EXIT
+          run --silence nix-store --realise "$newGenPath" --add-root "$newGenGcPath"
+
           ${activationCmds}
+
+          ${optionalString (!config.uninstall) ''
+            # Create the "current generation" GC root.
+            run --silence nix-store --realise "$newGenPath" --add-root "$currentGenGcPath"
+
+            if [[ -e "$legacyGenGcPath" ]]; then
+              run rm $VERBOSE_ARG "$legacyGenGcPath"
+            fi
+          ''}
         '';
       in
         pkgs.runCommand
diff --git a/modules/lib-bash/activation-init.sh b/modules/lib-bash/activation-init.sh
index 91111e5d0d29..b16d8741b917 100755
--- a/modules/lib-bash/activation-init.sh
+++ b/modules/lib-bash/activation-init.sh
@@ -59,34 +59,13 @@ function setupVars() {
     declare -gr hmDataPath="${XDG_DATA_HOME:-$HOME/.local/share}/home-manager"
     declare -gr genProfilePath="$profilesDir/home-manager"
     declare -gr newGenPath="@GENERATION_DIR@";
-    declare -gr newGenGcPath="$hmGcrootsDir/current-home"
+    declare -gr newGenGcPath="$hmGcrootsDir/new-home"
+    declare -gr currentGenGcPath="$hmGcrootsDir/current-home"
     declare -gr legacyGenGcPath="$globalGcrootsDir/current-home"
 
-    declare greatestGenNum
-    greatestGenNum=$( \
-        nix-env --list-generations --profile "$genProfilePath" \
-            | tail -1 \
-            | sed -E 's/ *([[:digit:]]+) .*/\1/')
-
-    if [[ -n $greatestGenNum ]] ; then
-        declare -gr oldGenNum=$greatestGenNum
-        declare -gr newGenNum=$((oldGenNum + 1))
-    else
-        declare -gr newGenNum=1
-    fi
-
-    if [[ -e $genProfilePath ]] ; then
+    if [[ -e $currentGenGcPath ]] ; then
         declare -g oldGenPath
-        oldGenPath="$(readlink -e "$genProfilePath")"
-    fi
-
-    _iVerbose "Sanity checking oldGenNum and oldGenPath"
-    if [[ -v oldGenNum && ! -v oldGenPath
-            || ! -v oldGenNum && -v oldGenPath ]]; then
-        _i $'The previous generation number and path are in conflict! These\nmust be either both empty or both set but are now set to\n\n    \'%s\' and \'%s\'\n\nIf you don\'t mind losing previous profile generations then\nthe easiest solution is probably to run\n\n   rm %s/home-manager*\n   rm %s/current-home\n\nand trying home-manager switch again. Good luck!' \
-           "${oldGenNum:-}" "${oldGenPath:-}" \
-           "$profilesDir" "$hmGcrootsDir"
-        exit 1
+        oldGenPath="$(readlink -e "$currentGenGcPath")"
     fi
 }
 
@@ -181,15 +160,13 @@ if [[ -v VERBOSE ]]; then
 fi
 
 _iVerbose "Activation variables:"
-if [[ -v oldGenNum ]] ; then
-    verboseEcho "  oldGenNum=$oldGenNum"
+if [[ -v oldGenPath ]] ; then
     verboseEcho "  oldGenPath=$oldGenPath"
 else
-    verboseEcho "  oldGenNum undefined (first run?)"
     verboseEcho "  oldGenPath undefined (first run?)"
 fi
 verboseEcho "  newGenPath=$newGenPath"
-verboseEcho "  newGenNum=$newGenNum"
 verboseEcho "  genProfilePath=$genProfilePath"
 verboseEcho "  newGenGcPath=$newGenGcPath"
+verboseEcho "  currentGenGcPath=$currentGenGcPath"
 verboseEcho "  legacyGenGcPath=$legacyGenGcPath"
diff --git a/modules/po/hm-modules.pot b/modules/po/hm-modules.pot
index 7a33a805a218..174fb3eb7727 100644
--- a/modules/po/hm-modules.pot
+++ b/modules/po/hm-modules.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Home Manager Modules\n"
 "Report-Msgid-Bugs-To: https://github.com/nix-community/home-manager/issues\n"
-"POT-Creation-Date: 2024-04-17 23:19+0200\n"
+"POT-Creation-Date: 2025-01-03 09:09+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -17,23 +17,23 @@ msgstr ""
 "Content-Type: text/plain; charset=CHARSET\n"
 "Content-Transfer-Encoding: 8bit\n"
 
-#: modules/files.nix:191
+#: modules/files.nix:188
 msgid "Creating home file links in %s"
 msgstr ""
 
-#: modules/files.nix:204
+#: modules/files.nix:201
 msgid "Cleaning up orphan links from %s"
 msgstr ""
 
-#: modules/files.nix:220
-msgid "Creating profile generation %s"
+#: modules/home-environment.nix:591
+msgid "Creating new profile generation"
 msgstr ""
 
-#: modules/files.nix:237
-msgid "No change so reusing latest profile generation %s"
+#: modules/home-environment.nix:594
+msgid "No change so reusing latest profile generation"
 msgstr ""
 
-#: modules/home-environment.nix:634
+#: modules/home-environment.nix:643
 msgid ""
 "Oops, Nix failed to install your new Home Manager profile!\n"
 "\n"
@@ -49,7 +49,7 @@ msgid ""
 "Then try activating your Home Manager configuration again."
 msgstr ""
 
-#: modules/home-environment.nix:667
+#: modules/home-environment.nix:676
 msgid "Activating %s"
 msgstr ""
 
@@ -61,54 +61,34 @@ msgstr ""
 msgid "Could not find suitable profile directory, tried %s and %s"
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:83
-msgid "Sanity checking oldGenNum and oldGenPath"
-msgstr ""
-
-#: modules/lib-bash/activation-init.sh:86
-msgid ""
-"The previous generation number and path are in conflict! These\n"
-"must be either both empty or both set but are now set to\n"
-"\n"
-"    '%s' and '%s'\n"
-"\n"
-"If you don't mind losing previous profile generations then\n"
-"the easiest solution is probably to run\n"
-"\n"
-"   rm %s/home-manager*\n"
-"   rm %s/current-home\n"
-"\n"
-"and trying home-manager switch again. Good luck!"
-msgstr ""
-
-#: modules/lib-bash/activation-init.sh:127
+#: modules/lib-bash/activation-init.sh:106
 msgid "Error: USER is set to \"%s\" but we expect \"%s\""
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:136
+#: modules/lib-bash/activation-init.sh:115
 msgid "Error: HOME is set to \"%s\" but we expect \"%s\""
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:153
+#: modules/lib-bash/activation-init.sh:132
 msgid "Starting Home Manager activation"
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:157
+#: modules/lib-bash/activation-init.sh:136
 msgid "Sanity checking Nix"
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:170
+#: modules/lib-bash/activation-init.sh:149
 msgid "This is a dry run"
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:174
+#: modules/lib-bash/activation-init.sh:153
 msgid "This is a live run"
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:180
+#: modules/lib-bash/activation-init.sh:159
 msgid "Using Nix version: %s"
 msgstr ""
 
-#: modules/lib-bash/activation-init.sh:183
+#: modules/lib-bash/activation-init.sh:162
 msgid "Activation variables:"
 msgstr ""
diff --git a/tests/integration/standalone/flake-basics.nix b/tests/integration/standalone/flake-basics.nix
index 4ce95997ca89..01f6571c76ba 100644
--- a/tests/integration/standalone/flake-basics.nix
+++ b/tests/integration/standalone/flake-basics.nix
@@ -49,6 +49,12 @@
     # Create a persistent login so that Alice has a systemd session.
     login_as_alice()
 
+    # Make sure that Alice has a "nix profile" compatible profile.
+    if True:
+      succeed_as_alice("nix profile install nixpkgs#cowsay")
+      result = succeed_as_alice("cowsay Hello")
+      machine.log(f"\n{result}")
+
     with subtest("Home Manager installation"):
       succeed_as_alice("nix run home-manager -- init --home-manager-url home-manager --nixpkgs-url nixpkgs --switch")