diff --git a/compiler/ir/backend.jvm/entrypoint/src/org/jetbrains/kotlin/backend/jvm/JvmIrCodegenFactory.kt b/compiler/ir/backend.jvm/entrypoint/src/org/jetbrains/kotlin/backend/jvm/JvmIrCodegenFactory.kt
index 10f3fed5e9b..52e28169fb8 100644
--- a/compiler/ir/backend.jvm/entrypoint/src/org/jetbrains/kotlin/backend/jvm/JvmIrCodegenFactory.kt
+++ b/compiler/ir/backend.jvm/entrypoint/src/org/jetbrains/kotlin/backend/jvm/JvmIrCodegenFactory.kt
@@ -163,7 +163,7 @@ open class JvmIrCodegenFactory(
 
         SourceDeclarationsPreprocessor(psi2irContext).run(input.files)
 
-        if (pluginExtensions.isNotEmpty()) {
+        if (pluginExtensions.isNotEmpty() && psi2irContext.configuration.generateBodies) {
             // The plugin context contains unbound symbols right after construction and has to be
             // instantiated before we resolve unbound symbols and invoke any postprocessing steps.
             val pluginContext = IrPluginContextImpl(
diff --git a/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/JvmCompilerWithKaptFacade.kt b/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/JvmCompilerWithKaptFacade.kt
index 35a9223e3e8..cf50ca89577 100644
--- a/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/JvmCompilerWithKaptFacade.kt
+++ b/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/JvmCompilerWithKaptFacade.kt
@@ -5,6 +5,7 @@
 
 package org.jetbrains.kotlin.kapt3.test
 
+import org.jetbrains.kotlin.backend.common.extensions.IrGenerationExtension
 import org.jetbrains.kotlin.codegen.ClassBuilderMode
 import org.jetbrains.kotlin.codegen.GenerationUtils
 import org.jetbrains.kotlin.codegen.OriginCollectingClassBuilderFactory
@@ -13,7 +14,10 @@ import org.jetbrains.kotlin.kapt3.util.MessageCollectorBackedKaptLogger
 import org.jetbrains.kotlin.test.model.*
 import org.jetbrains.kotlin.test.services.*
 
-class JvmCompilerWithKaptFacade(private val testServices: TestServices) :
+class JvmCompilerWithKaptFacade(
+    private val testServices: TestServices,
+    private val additionalPluginExtension: IrGenerationExtension? = null,
+) :
     AbstractTestFacade<ResultingArtifact.Source, KaptContextBinaryArtifact>() {
     override val inputKind: TestArtifactKind<ResultingArtifact.Source>
         get() = SourcesKind
@@ -26,6 +30,9 @@ class JvmCompilerWithKaptFacade(private val testServices: TestServices) :
     override fun transform(module: TestModule, inputArtifact: ResultingArtifact.Source): KaptContextBinaryArtifact {
         val configurationProvider = testServices.compilerConfigurationProvider
         val project = configurationProvider.getProject(module)
+        if (additionalPluginExtension != null) {
+            IrGenerationExtension.registerExtension(project, additionalPluginExtension)
+        }
         val ktFiles = testServices.sourceFileProvider.getKtFilesForSourceFiles(module.files, project, findViaVfs = true).values.toList()
         val classBuilderFactory = OriginCollectingClassBuilderFactory(ClassBuilderMode.KAPT3)
         val generationState = GenerationUtils.compileFiles(
diff --git a/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestBase.kt b/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestBase.kt
index 32a1a803941..60abcccc440 100644
--- a/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestBase.kt
+++ b/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestBase.kt
@@ -6,7 +6,10 @@
 package org.jetbrains.kotlin.kapt3.test.integration
 
 import org.jetbrains.kotlin.analyzer.CompilationErrorException
+import org.jetbrains.kotlin.backend.common.extensions.IrGenerationExtension
+import org.jetbrains.kotlin.backend.common.extensions.IrPluginContext
 import org.jetbrains.kotlin.cli.common.messages.CompilerMessageSeverity
+import org.jetbrains.kotlin.ir.declarations.IrModuleFragment
 import org.jetbrains.kotlin.kapt3.javac.KaptJavaFileObject
 import org.jetbrains.kotlin.test.services.JUnit5Assertions.assertEquals
 import org.jetbrains.kotlin.test.services.JUnit5Assertions.assertTrue
@@ -14,6 +17,7 @@ import org.jetbrains.kotlin.test.TargetBackend
 import org.jetbrains.kotlin.test.services.JUnit5Assertions.assertNotNull
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.TestInfo
+import org.junit.jupiter.api.fail
 import java.io.File
 import javax.annotation.processing.ProcessingEnvironment
 import javax.annotation.processing.RoundEnvironment
@@ -38,6 +42,7 @@ abstract class AbstractKotlinKapt3IntegrationTestBase(private val testInfo: Test
         vararg supportedAnnotations: String,
         options: Map<String, String> = emptyMap(),
         expectFailure: Boolean = false,
+        additionalPluginExtension: IrGenerationExtension? = null,
         process: (Set<TypeElement>, RoundEnvironment, ProcessingEnvironment, Kapt3ExtensionForTests) -> Unit
     ) {
         val file = File(TEST_DATA_DIR, "$name.kt")
@@ -45,6 +50,7 @@ abstract class AbstractKotlinKapt3IntegrationTestBase(private val testInfo: Test
             targetBackend,
             options,
             supportedAnnotations.toList(),
+            additionalPluginExtension,
             process
         ).apply {
             initTestInfo(testInfo)
@@ -241,4 +247,14 @@ abstract class AbstractKotlinKapt3IntegrationTestBase(private val testInfo: Test
         diagnostics.assertContainsDiagnostic("warning: a warning from processor", CompilerMessageSeverity.STRONG_WARNING)
         diagnostics.assertContainsDiagnostic("Note: a note from processor", CompilerMessageSeverity.INFO)
     }
-}
\ No newline at end of file
+
+    @Test
+    fun testKt54245() = test(
+        "Simple", "test.MyAnnotation",
+        additionalPluginExtension = object : IrGenerationExtension {
+            override fun generate(moduleFragment: IrModuleFragment, pluginContext: IrPluginContext) {
+                fail("IR generation extensions should not be run in kapt mode.")
+            }
+        }
+    ) { _, _, _, _ -> }
+}
diff --git a/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestRunner.kt b/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestRunner.kt
index 0e659d1e6a5..5487652945c 100644
--- a/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestRunner.kt
+++ b/plugins/kapt3/kapt3-compiler/test/org/jetbrains/kotlin/kapt3/test/integration/AbstractKotlinKapt3IntegrationTestRunner.kt
@@ -5,6 +5,7 @@
 
 package org.jetbrains.kotlin.kapt3.test.integration
 
+import org.jetbrains.kotlin.backend.common.extensions.IrGenerationExtension
 import org.jetbrains.kotlin.kapt3.test.JvmCompilerWithKaptFacade
 import org.jetbrains.kotlin.kapt3.test.KaptContextBinaryArtifact
 import org.jetbrains.kotlin.kapt3.test.KaptEnvironmentConfigurator
@@ -27,6 +28,7 @@ class AbstractKotlinKapt3IntegrationTestRunner(
     targetBackend: TargetBackend,
     private val processorOptions: Map<String, String>,
     private val supportedAnnotations: List<String>,
+    private val additionalPluginExtension: IrGenerationExtension?,
     private val process: (Set<TypeElement>, RoundEnvironment, ProcessingEnvironment, Kapt3ExtensionForTests) -> Unit
 ) : AbstractKotlinCompilerWithTargetBackendTest(targetBackend) {
 
@@ -55,7 +57,7 @@ class AbstractKotlinKapt3IntegrationTestRunner(
             { KaptIntegrationEnvironmentConfigurator(it, processorOptions, supportedAnnotations, process) }
         )
 
-        facadeStep(::JvmCompilerWithKaptFacade)
+        facadeStep { services -> JvmCompilerWithKaptFacade(services, additionalPluginExtension) }
         handlersStep(KaptContextBinaryArtifact.Kind) {
             useHandlers(::KaptIntegrationStubsDumpHandler, ::ProcessorWasCalledHandler)
         }