diff --git a/analysis/analysis-api-standalone/analysis-api-standalone-native/build.gradle.kts b/analysis/analysis-api-standalone/analysis-api-standalone-native/build.gradle.kts
index 7193e9535ea..123c6580d8c 100644
--- a/analysis/analysis-api-standalone/analysis-api-standalone-native/build.gradle.kts
+++ b/analysis/analysis-api-standalone/analysis-api-standalone-native/build.gradle.kts
@@ -2,7 +2,6 @@ import org.jetbrains.kotlin.kotlinNativeDist
 
 plugins {
     kotlin("jvm")
-    id("jps-compatible")
 }
 
 dependencies {
diff --git a/analysis/low-level-api-fir/low-level-api-fir-native/build.gradle.kts b/analysis/low-level-api-fir/low-level-api-fir-native/build.gradle.kts
index 4fbdc7942b7..092a39e8ef2 100644
--- a/analysis/low-level-api-fir/low-level-api-fir-native/build.gradle.kts
+++ b/analysis/low-level-api-fir/low-level-api-fir-native/build.gradle.kts
@@ -1,6 +1,5 @@
 plugins {
     kotlin("jvm")
-    id("jps-compatible")
 }
 
 dependencies {
diff --git a/generators/sir-tests-generator/build.gradle.kts b/generators/sir-tests-generator/build.gradle.kts
index 6dd1578c5b6..72063e589a2 100644
--- a/generators/sir-tests-generator/build.gradle.kts
+++ b/generators/sir-tests-generator/build.gradle.kts
@@ -1,6 +1,5 @@
 plugins {
     kotlin("jvm")
-    id("jps-compatible")
 }
 
 sourceSets {
diff --git a/libraries/tools/kotlinp/build.gradle.kts b/libraries/tools/kotlinp/build.gradle.kts
index e125da7682b..782fb7e2617 100644
--- a/libraries/tools/kotlinp/build.gradle.kts
+++ b/libraries/tools/kotlinp/build.gradle.kts
@@ -5,6 +5,7 @@ description = "kotlinp"
 
 plugins {
     kotlin("jvm")
+    id("jps-compatible")
 }
 
 val kotlinpAsmVersion = "9.0"
diff --git a/native/executors/build.gradle.kts b/native/executors/build.gradle.kts
index 18ba0a73f56..e0c0cd9b2fd 100644
--- a/native/executors/build.gradle.kts
+++ b/native/executors/build.gradle.kts
@@ -10,6 +10,14 @@ plugins {
     kotlin("jvm")
 }
 
+val isNativeBuildToolsProject = rootProject.name == "native-build-tools"
+
+if (!isNativeBuildToolsProject) {
+    // The module is shared between the main project and 'native-build-tools',
+    // in which there is no 'jps-compatible' plugin configured.
+    apply(plugin = "jps-compatible")
+}
+
 repositories {
     mavenCentral()
 }
@@ -29,7 +37,7 @@ dependencies {
 
     // KT-61897: Workaround for https://github.com/gradle/gradle/issues/26358
     // (wrong conflict resolution, causing selection of not the latest version of `:kotlin-util-klib` module)
-    if (rootProject.name == "native-build-tools") {
+    if (isNativeBuildToolsProject) {
         implementation("org.jetbrains.kotlin:kotlin-native-utils:${project.bootstrapKotlinVersion}")
     } else {
         implementation(project(":native:kotlin-native-utils"))
diff --git a/repo/artifacts-tests/build.gradle.kts b/repo/artifacts-tests/build.gradle.kts
index eb68592f946..d0e6c2ae3a5 100644
--- a/repo/artifacts-tests/build.gradle.kts
+++ b/repo/artifacts-tests/build.gradle.kts
@@ -2,7 +2,6 @@ import java.nio.file.Paths
 
 plugins {
     kotlin("jvm")
-    id("jps-compatible")
 }
 
 dependencies {