diff --git a/cmake/QtBuildInformation.cmake b/cmake/QtBuildInformation.cmake
index 6929f9134ef..f9495bb0d26 100644
--- a/cmake/QtBuildInformation.cmake
+++ b/cmake/QtBuildInformation.cmake
@@ -111,6 +111,12 @@ from the build directory")
     if(QT_SUPERBUILD)
         qt_internal_save_previously_visited_packages()
     endif()
+
+    # TODO: Abuse qt_print_build_instructions being called as the last command in a top-level build.
+    # Instead we should call this explicitly at the end of the top-level project.
+    if(QT_SUPERBUILD)
+        qt_internal_qt_configure_end()
+    endif()
 endfunction()
 
 function(qt_configure_print_summary_helper summary_reports force_show)
diff --git a/cmake/QtBuildInternals/QtBuildInternalsConfig.cmake b/cmake/QtBuildInternals/QtBuildInternalsConfig.cmake
index 3bdb6488318..1067e01e835 100644
--- a/cmake/QtBuildInternals/QtBuildInternalsConfig.cmake
+++ b/cmake/QtBuildInternals/QtBuildInternalsConfig.cmake
@@ -131,9 +131,10 @@ function(qt_build_internals_disable_pkg_config_if_needed)
     endif()
 
     # Features won't have been evaluated yet if this is the first run, have to evaluate this here
-    if ((NOT DEFINED "FEATURE_pkg_config") AND (DEFINED "INPUT_pkg_config")
-            AND (NOT "${INPUT_pkg_config}" STREQUAL "undefined")
-            AND (NOT "${INPUT_pkg_config}" STREQUAL ""))
+    if((NOT DEFINED "FEATURE_pkg_config" OR QT_INTERNAL_CALLED_FROM_CONFIGURE)
+            AND DEFINED INPUT_pkg_config
+            AND NOT "${INPUT_pkg_config}" STREQUAL "undefined"
+            AND NOT "${INPUT_pkg_config}" STREQUAL "")
         if(INPUT_pkg_config)
             set(FEATURE_pkg_config ON)
         else()
@@ -603,9 +604,27 @@ macro(qt_build_repo_end)
         set(QT_INTERNAL_FRESH_REQUESTED "FALSE" CACHE INTERNAL "")
     endif()
 
+    if(NOT QT_SUPERBUILD)
+        qt_internal_qt_configure_end()
+    endif()
+
     list(POP_BACK CMAKE_MESSAGE_CONTEXT)
 endmacro()
 
+# Function called either at the end of per-repo configuration, or at the end of configuration of
+# a super build.
+# At the moment it is called before examples are configured in a per-repo build. We might want
+# to change that at some point if needed.
+function(qt_internal_qt_configure_end)
+    # If Qt is configued via the configure script, remove the marker variable, so that any future
+    # reconfigurations that are done by calling cmake directly don't trigger configure specific
+    # logic.
+    unset(QT_INTERNAL_CALLED_FROM_CONFIGURE CACHE)
+
+    # Clean up stale feature input values.
+    qt_internal_clean_feature_inputs()
+endfunction()
+
 macro(qt_build_repo)
     qt_build_repo_begin(${ARGN})
 
diff --git a/cmake/QtFeature.cmake b/cmake/QtFeature.cmake
index 93f1ed81031..77b91e077cb 100644
--- a/cmake/QtFeature.cmake
+++ b/cmake/QtFeature.cmake
@@ -410,10 +410,15 @@ function(qt_evaluate_feature feature)
         qt_evaluate_config_expression(emit_if ${arg_EMIT_IF})
     endif()
 
-    # If FEATURE_ is not defined trying to use INPUT_ variable to enable/disable feature.
-    if ((NOT DEFINED "FEATURE_${feature}") AND (DEFINED "INPUT_${feature}")
-        AND (NOT "${INPUT_${feature}}" STREQUAL "undefined")
-        AND (NOT "${INPUT_${feature}}" STREQUAL ""))
+    # If FEATURE_ is not defined try to use the INPUT_ variable to enable/disable feature.
+    # If FEATURE_ is defined and the configure script is being used (so
+    # QT_INTERNAL_CALLED_FROM_CONFIGURE is TRUE), ignore the FEATURE_ variable, and take into
+    # account the INPUT_ variable instead, because a command line argument takes priority over
+    # a pre-cached FEATURE_ variable.
+    if((NOT DEFINED FEATURE_${feature} OR QT_INTERNAL_CALLED_FROM_CONFIGURE)
+        AND DEFINED INPUT_${feature}
+        AND NOT "${INPUT_${feature}}" STREQUAL "undefined"
+        AND NOT "${INPUT_${feature}}" STREQUAL "")
         if(INPUT_${feature})
             set(FEATURE_${feature} ON)
         else()
@@ -906,6 +911,18 @@ function(qt_internal_detect_dirty_features)
     endif()
 endfunction()
 
+function(qt_internal_clean_feature_inputs)
+    foreach(feature IN LISTS QT_KNOWN_FEATURES)
+        # Unset the INPUT_foo cache variables after they were used in feature evaluation, to
+        # ensure stale values don't influence features upon reconfiguration when
+        # QT_INTERNAL_CALLED_FROM_CONFIGURE is TRUE and the INPUT_foo variable is not passed.
+        # e.g. first configure -no-gui, then manually toggle FEATURE_gui to ON in
+        # CMakeCache.txt, then reconfigure (with the configure script) without -no-gui.
+        # Without this unset(), we'd have switched FEATURE_gui to OFF again.
+        unset(INPUT_${feature} CACHE)
+    endforeach()
+endfunction()
+
 function(qt_config_compile_test name)
     if(DEFINED "TEST_${name}")
         return()
diff --git a/cmake/QtProcessConfigureArgs.cmake b/cmake/QtProcessConfigureArgs.cmake
index 995f64a95fc..f8f6d309810 100644
--- a/cmake/QtProcessConfigureArgs.cmake
+++ b/cmake/QtProcessConfigureArgs.cmake
@@ -179,6 +179,10 @@ else()
     set(multi_config OFF)
 endif()
 
+# Tell the build system we are configuring via the configure script so we can act on that.
+# The cache variable is unset at the end of configuration.
+push("-DQT_INTERNAL_CALLED_FROM_CONFIGURE:BOOL=TRUE")
+
 if(FRESH_REQUESTED)
     push("-DQT_INTERNAL_FRESH_REQUESTED:BOOL=TRUE")
     if(CMAKE_VERSION VERSION_GREATER_EQUAL "3.24")
diff --git a/cmake/QtSetup.cmake b/cmake/QtSetup.cmake
index 5c9e56e6e6a..dfad3e77061 100644
--- a/cmake/QtSetup.cmake
+++ b/cmake/QtSetup.cmake
@@ -14,8 +14,10 @@ if(NOT QT_INTERNAL_IS_STANDALONE_TEST)
         "When this is present and set to true, it signals that we are building Qt from source.")
 endif()
 
-# Pre-calculate the developer_build feature if it's set by the user via INPUT_developer_build
-if(NOT DEFINED FEATURE_developer_build
+# Pre-calculate the developer_build feature if it's set by the user via the INPUT_developer_build
+# variable when using the configure script. When not using configure, don't take the INPUT variable
+# into account, so that users can toggle the feature directly in the cache or via IDE.
+if((NOT DEFINED FEATURE_developer_build OR QT_INTERNAL_CALLED_FROM_CONFIGURE)
         AND DEFINED INPUT_developer_build
         AND NOT "${INPUT_developer_build}" STREQUAL "undefined"
         AND NOT "${INPUT_developer_build}" STREQUAL "")
@@ -28,7 +30,7 @@ endif()
 
 # Pre-calculate the no_prefix feature if it's set by configure via INPUT_no_prefix.
 # This needs to be done before qtbase/configure.cmake is processed.
-if(NOT DEFINED FEATURE_no_prefix
+if((NOT DEFINED FEATURE_no_prefix OR QT_INTERNAL_CALLED_FROM_CONFIGURE)
         AND DEFINED INPUT_no_prefix
         AND NOT "${INPUT_no_prefix}" STREQUAL "undefined"
         AND NOT "${INPUT_no_prefix}" STREQUAL "")