diff --git a/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleConfiguration.java b/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleConfiguration.java
index 4c9ab621a..ac4c1f1b5 100644
--- a/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleConfiguration.java
+++ b/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleConfiguration.java
@@ -40,6 +40,11 @@ public class ModuleConfiguration {
   public final Path scannerConfig;
   /** Directory where all serialized data from checkers are located. */
   public final Path dir;
+  /**
+   * Global unique ID for this module. 0 is for the target module, and the i-th module is for the
+   * i-th downstream dependency.
+   */
+  public final int id;
 
   /**
    * Creates an instance of {@link ModuleConfiguration} from the given json object.
@@ -63,6 +68,7 @@ public static ModuleConfiguration buildFromJson(int id, Path globalDir, JSONObje
   public ModuleConfiguration(int id, Path globalDir, Path checkerConfig, Path scannerConfig) {
     this.checkerConfig = checkerConfig;
     this.scannerConfig = scannerConfig;
+    this.id = id;
     this.dir = globalDir.resolve(String.valueOf(id));
     try {
       Files.deleteIfExists(this.dir);
diff --git a/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleInfo.java b/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleInfo.java
index 436947af4..bf3c7577e 100644
--- a/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleInfo.java
+++ b/annotator-core/src/main/java/edu/ucr/cs/riple/core/module/ModuleInfo.java
@@ -36,7 +36,9 @@
 import edu.ucr.cs.riple.core.util.Utility;
 import edu.ucr.cs.riple.injector.location.Location;
 import edu.ucr.cs.riple.injector.location.OnClass;
+import edu.ucr.cs.riple.scanner.Serializer;
 import edu.ucr.cs.riple.scanner.generatedcode.SourceType;
+import java.nio.file.Path;
 
 /** This class is used to store the code structural information about the module. */
 public class ModuleInfo {
@@ -87,6 +89,7 @@ public ModuleInfo(
     // Build with scanner checker activated to generate required files to create the moduleInfo.
     context.checker.prepareConfigFilesForBuild(configurations);
     Utility.runScannerChecker(context, configurations, buildCommand);
+    checkScannerConfiguration();
     this.nonnullStore = new NonnullStore(configurations, context);
     this.fieldRegistry = new FieldRegistry(configurations, context);
     this.methodRegistry = new MethodRegistry(context);
@@ -202,4 +205,31 @@ public CompoundRegionRegistry getRegionRegistry() {
   public ImmutableSet<AnnotationProcessorHandler> getAnnotationProcessorHandlers() {
     return annotationProcessorHandlers;
   }
+
+  /** Checks if AnnotatorScanner is executed correctly for the modules. */
+  private void checkScannerConfiguration() {
+    for (ModuleConfiguration config : configurations) {
+      if (config.scannerConfig == null) {
+        throw new IllegalArgumentException(
+            "AnnotatorScanner configuration is not set for module: " + config);
+      }
+      // check for existence of one of the serialized files from Scanner. In this case we chose
+      // NON_NULL_ELEMENTS_FILE_NAME but any other file would work.
+      Path pathToNonnull = config.dir.resolve(Serializer.NON_NULL_ELEMENTS_FILE_NAME);
+      if (!pathToNonnull.toFile().exists()) {
+        String moduleName = config.id == 0 ? "target" : "dependency " + config.id;
+        throw new IllegalArgumentException(
+            "AnnotatorScanner is not correctly configured for the module: "
+                + moduleName
+                + ".\n"
+                + "Please verify that the path specified for AnnotatorScanner on line "
+                + config.id
+                + " in the configuration file matches the path provided in file with -cp/--config-paths, "
+                + "and that it is identical to the path specified with -XepOpt:AnnotatorScanner:ConfigPath."
+                + "\n"
+                + "If the path is set correctly, rerun annotator with -rboserr/--redirect-build-output-stderr flag "
+                + "and check compilation output and ensure NullAway and AnnotatorScanner is executing properly.");
+      }
+    }
+  }
 }