diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt
index 93ca0f42cc3..679dc6cd656 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt
@@ -19,6 +19,7 @@ package org.jetbrains.kotlin.gradle
 import org.gradle.api.logging.LogLevel
 import org.jetbrains.kotlin.gradle.plugin.MULTIPLE_KOTLIN_PLUGINS_LOADED_WARNING
 import org.jetbrains.kotlin.gradle.plugin.MULTIPLE_KOTLIN_PLUGINS_SPECIFIC_PROJECTS_WARNING
+import org.jetbrains.kotlin.gradle.scripting.internal.ScriptingGradleSubplugin
 import org.jetbrains.kotlin.gradle.tasks.USING_JVM_INCREMENTAL_COMPILATION_MESSAGE
 import org.jetbrains.kotlin.gradle.util.*
 import org.junit.Test
@@ -995,4 +996,12 @@ class KotlinGradleIT : BaseGradleIT() {
             assertSuccessful()
         }
     }
+
+    @Test
+    fun testNoScriptingWarning() = with(Project("simpleProject")) {
+        // KT-31124
+        build {
+            assertNotContains(ScriptingGradleSubplugin.MISCONFIGURATION_MESSAGE_SUFFIX)
+        }
+    }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
index 8ef9ec3ccdb..97ac8d10120 100755
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
@@ -569,9 +569,9 @@ internal open class KotlinPlugin(
         }
         (project.kotlinExtension as KotlinJvmProjectExtension).target = target
 
-        project.pluginManager.apply(ScriptingGradleSubplugin::class.java)
-
         super.apply(project)
+
+        project.pluginManager.apply(ScriptingGradleSubplugin::class.java)
     }
 }
 
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/scripting/internal/ScriptingGradleSubplugin.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/scripting/internal/ScriptingGradleSubplugin.kt
index 1d83b55da0e..d69910b24bc 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/scripting/internal/ScriptingGradleSubplugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/scripting/internal/ScriptingGradleSubplugin.kt
@@ -27,8 +27,6 @@ import org.jetbrains.kotlin.gradle.utils.isGradleVersionAtLeast
 import org.jetbrains.kotlin.scripting.definitions.ScriptDefinitionsFromClasspathDiscoverySource
 import java.io.File
 
-private const val MISCONFIGURATION_MESSAGE_SUFFIX = "the plugin is probably applied by a mistake"
-
 private const val MIN_SUPPORTED_GRADLE_MAJOR_VERSION = 5
 private const val MIN_SUPPORTED_GRADLE_MINOR_VERSION = 0
 
@@ -36,6 +34,8 @@ private const val SCRIPTING_LOG_PREFIX = "kotlin scripting plugin:"
 
 class ScriptingGradleSubplugin : Plugin<Project> {
     companion object {
+        const val MISCONFIGURATION_MESSAGE_SUFFIX = "the plugin is probably applied by a mistake"
+
         fun isEnabled(project: Project) = project.plugins.findPlugin(ScriptingGradleSubplugin::class.java) != null
 
         fun configureForSourceSet(project: Project, sourceSetName: String) {
@@ -44,6 +44,7 @@ class ScriptingGradleSubplugin : Plugin<Project> {
                 isCanBeConsumed = false
                 description = "Script filename extensions discovery classpath configuration"
             }
+            project.logger.info("$SCRIPTING_LOG_PREFIX created the scripting discovery configuration: ${discoveryConfiguration.name}")
 
             configureDiscoveryTransformation(project, discoveryConfiguration, getDiscoveryResultsConfigurationName(sourceSetName))
         }
@@ -61,14 +62,17 @@ class ScriptingGradleSubplugin : Plugin<Project> {
 
                         try {
                             val discoveryClasspathConfigurationName = getDiscoveryClasspathConfigurationName(task.sourceSetName)
-                            if (project.configurations.findByName(discoveryClasspathConfigurationName)?.allDependencies?.isEmpty() == false) {
-                                if (isGradleVersionAtLeast(MIN_SUPPORTED_GRADLE_MAJOR_VERSION, MIN_SUPPORTED_GRADLE_MINOR_VERSION)) {
-                                    configureScriptsExtensions(project, javaPluginConvention, task.sourceSetName)
-                                } else {
-                                    project.logger.warn("$SCRIPTING_LOG_PREFIX incompatible Gradle version. Please use the plugin with Gradle version $MIN_SUPPORTED_GRADLE_MAJOR_VERSION.$MIN_SUPPORTED_GRADLE_MINOR_VERSION or newer.")
+                            val discoveryClasspathConfiguration = project.configurations.findByName(discoveryClasspathConfigurationName)
+                            when {
+                                discoveryClasspathConfiguration == null ->
+                                    project.logger.warn("$SCRIPTING_LOG_PREFIX $project.${task.name} - configuration not found: $discoveryClasspathConfigurationName, $MISCONFIGURATION_MESSAGE_SUFFIX")
+                                discoveryClasspathConfiguration.allDependencies.isEmpty() -> {
+                                    // skip further checks - user did not configured any discovery sources
                                 }
-                            } else {
-                                project.logger.warn("$SCRIPTING_LOG_PREFIX $project.${task.name} - configuration not found: $discoveryClasspathConfigurationName, $MISCONFIGURATION_MESSAGE_SUFFIX")
+                                !isGradleVersionAtLeast(MIN_SUPPORTED_GRADLE_MAJOR_VERSION, MIN_SUPPORTED_GRADLE_MINOR_VERSION) ->
+                                    project.logger.warn("$SCRIPTING_LOG_PREFIX incompatible Gradle version. Please use the plugin with Gradle version $MIN_SUPPORTED_GRADLE_MAJOR_VERSION.$MIN_SUPPORTED_GRADLE_MINOR_VERSION or newer.")
+                                else ->
+                                    configureScriptsExtensions(project, javaPluginConvention, task.sourceSetName)
                             }
                         } catch (e: IllegalStateException) {
                             project.logger.warn("$SCRIPTING_LOG_PREFIX applied in the non-supported environment (error received: ${e.message})")