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 4b3510e3e7d..d58359d3136 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
@@ -1207,4 +1207,24 @@ class KotlinGradleIT : BaseGradleIT() {
             assertTrue(compiledKotlinClasses.isEmpty())
         }
     }
+
+    /** Regression test for KT-45787. **/
+    @Test
+    fun testPluginDoesNotUseDeprecatedConfigurationsForAssociatedDependencies() {
+        with(
+            Project(
+                projectName = "associatedDependencies",
+                minLogLevel = LogLevel.INFO
+            )
+        ) {
+            setupWorkingDir()
+
+            build(
+                "tasks",
+                options = defaultBuildOptions().copy(warningMode = WarningMode.Fail)
+            ) {
+                assertSuccessful()
+            }
+        }
+    }
 }
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/associatedDependencies/build.gradle b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/associatedDependencies/build.gradle
new file mode 100644
index 00000000000..dcea7225fea
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/associatedDependencies/build.gradle
@@ -0,0 +1,29 @@
+plugins {
+    id "org.jetbrains.kotlin.jvm"
+}
+
+sourceSets {
+    integrationTest {
+        kotlin {
+            srcDirs += "src/integrationTest/kotlin"
+        }
+        java {
+            srcDirs += "src/integrationTest/java"
+        }
+        resources {
+            srcDirs += "src/integrationTest/resources"
+        }
+        compileClasspath += main.output + test.output
+        runtimeClasspath += main.output + test.output
+    }
+}
+
+kotlin {
+    target {
+        java
+        compilations.integrationTest {
+            associateWith compilations.main
+            associateWith compilations.test
+        }
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/associatedDependencies/settings.gradle b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/associatedDependencies/settings.gradle
new file mode 100644
index 00000000000..de7969b173a
--- /dev/null
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/associatedDependencies/settings.gradle
@@ -0,0 +1,11 @@
+pluginManagement {
+    repositories {
+        mavenLocal()
+        mavenCentral()
+        gradlePluginPortal()
+    }
+
+    plugins {
+        id "org.jetbrains.kotlin.jvm" version "$kotlin_version"
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/kotlinCompilations.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/kotlinCompilations.kt
index a75801a914d..2635bdf5bed 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/kotlinCompilations.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/kotlinCompilations.kt
@@ -253,18 +253,23 @@ abstract class AbstractKotlinCompilation<T : KotlinCommonOptions>(
     }
 
     protected open fun addAssociateCompilationDependencies(other: KotlinCompilation<*>) {
-        target.project.dependencies.run {
-            val project = target.project
+        with(target.project) {
 
-            add(
-                compileDependencyConfigurationName,
-                project.files(Callable { other.output.classesDirs }, Callable { other.compileDependencyFiles })
+            dependencies.add(
+                compileOnlyConfigurationName,
+                project.files(Callable { other.output.classesDirs })
             )
 
+            configurations.named(compileOnlyConfigurationName).configure {
+                it.extendsFrom(configurations.findByName(other.compileDependencyConfigurationName))
+            }
+
             if (this@AbstractKotlinCompilation is KotlinCompilationToRunnableFiles<*>) {
-                add(runtimeDependencyConfigurationName, project.files(Callable { other.output.allOutputs }))
+                dependencies.add(runtimeOnlyConfigurationName, project.files(Callable { other.output.allOutputs }))
                 if (other is KotlinCompilationToRunnableFiles<*>) {
-                    add(runtimeDependencyConfigurationName, project.files(Callable { other.runtimeDependencyFiles }))
+                    configurations.named(runtimeOnlyConfigurationName).configure {
+                        it.extendsFrom(configurations.findByName(other.runtimeDependencyConfigurationName))
+                    }
                 }
             }
         }