diff --git a/src/main/java/com/jfrog/ide/idea/scan/ScanUtils.java b/src/main/java/com/jfrog/ide/idea/scan/ScanUtils.java
index fab31beb..5022cacb 100644
--- a/src/main/java/com/jfrog/ide/idea/scan/ScanUtils.java
+++ b/src/main/java/com/jfrog/ide/idea/scan/ScanUtils.java
@@ -6,14 +6,13 @@
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.project.ProjectUtil;
 import com.intellij.openapi.vfs.VirtualFile;
+import com.jfrog.ide.common.utils.Utils;
 import com.jfrog.ide.idea.log.Logger;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.SystemUtils;
 
 import java.io.IOException;
 import java.nio.file.Path;
-import java.util.Collection;
-import java.util.Map;
 import java.util.Set;
 
 /**
@@ -22,14 +21,12 @@
 public class ScanUtils {
     /**
      * This method gets a set of modules from IDEA, and searches for projects to be scanned.
-     * It appends the root path of each module it finds into a set.
      *
-     * @param scannersMap - current scanners
-     * @param project     - the project
+     * @param project - the project
      * @return local scan paths
      */
-    static Set<Path> createScanPaths(Map<Integer, ScannerBase> scannersMap, Project project) {
-        final Set<Path> paths = Sets.newHashSet();
+    public static Set<Path> createScanPaths(Project project) {
+        Set<Path> paths = Sets.newHashSet();
         paths.add(com.jfrog.ide.idea.utils.Utils.getProjectBasePath(project));
         for (Module module : ModuleManager.getInstance(project).getModules()) {
             VirtualFile modulePath = ProjectUtil.guessModuleDir(module);
@@ -37,7 +34,7 @@ static Set<Path> createScanPaths(Map<Integer, ScannerBase> scannersMap, Project
                 paths.add(modulePath.toNioPath());
             }
         }
-        scannersMap.values().stream().map(ScannerBase::getProjectPaths).flatMap(Collection::stream).forEach(paths::add);
+        paths = Utils.consolidatePaths(paths);
         Logger.getInstance().debug("Scanning projects in the following paths: " + paths);
         return paths;
     }
diff --git a/src/main/java/com/jfrog/ide/idea/scan/ScannerFactory.java b/src/main/java/com/jfrog/ide/idea/scan/ScannerFactory.java
index 63755203..3fa120a1 100644
--- a/src/main/java/com/jfrog/ide/idea/scan/ScannerFactory.java
+++ b/src/main/java/com/jfrog/ide/idea/scan/ScannerFactory.java
@@ -15,6 +15,7 @@
 
 import java.io.IOException;
 import java.nio.file.Path;
+import java.util.Collection;
 import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.ExecutorService;
@@ -45,7 +46,8 @@ public Map<Integer, ScannerBase> refreshScanners(Map<Integer, ScannerBase> oldSc
         Map<Integer, ScannerBase> scanners = Maps.newHashMap();
         refreshMavenScanner(scanners, oldScanners, executor, scanLogic);
         refreshPypiScanners(scanners, oldScanners, executor, scanLogic);
-        Set<Path> scanPaths = createScanPaths(oldScanners, project);
+        Set<Path> scanPaths = createScanPaths(project);
+        oldScanners.values().stream().map(ScannerBase::getProjectPaths).flatMap(Collection::stream).forEach(scanPaths::add);
         refreshGenericScanners(scanners, oldScanners, scanPaths, executor, scanLogic);
         return scanners;
     }
diff --git a/src/main/java/com/jfrog/ide/idea/scan/data/applications/JFrogApplicationsConfig.java b/src/main/java/com/jfrog/ide/idea/scan/data/applications/JFrogApplicationsConfig.java
index 158257da..dde08b0a 100644
--- a/src/main/java/com/jfrog/ide/idea/scan/data/applications/JFrogApplicationsConfig.java
+++ b/src/main/java/com/jfrog/ide/idea/scan/data/applications/JFrogApplicationsConfig.java
@@ -3,14 +3,16 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.intellij.openapi.project.Project;
 import com.jfrog.ide.idea.configuration.GlobalSettings;
+import com.jfrog.ide.idea.scan.ScanUtils;
 import lombok.Getter;
 import lombok.NoArgsConstructor;
 
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
 
 import static com.jfrog.ide.idea.scan.SourceCodeScannerManager.convertToSkippedFolders;
-import static com.jfrog.ide.idea.utils.Utils.getProjectBasePath;
 
 @Getter
 @NoArgsConstructor
@@ -22,15 +24,16 @@ public class JFrogApplicationsConfig {
 
     public static JFrogApplicationsConfig createApplicationConfigWithDefaultModule(Project project) {
         JFrogApplicationsConfig applicationsConfig = new JFrogApplicationsConfig();
-
-        ModuleConfig defualtModuleConfig = new ModuleConfig();
-        defualtModuleConfig.setSourceRoot(getProjectBasePath(project).toAbsolutePath().toString());
-        defualtModuleConfig.setExcludePatterns(convertToSkippedFolders(GlobalSettings.getInstance().getServerConfig().getExcludedPaths()));
-
+        Set<Path> paths = ScanUtils.createScanPaths(project);
         applicationsConfig.modules = new ArrayList<>();
-        applicationsConfig.modules.add(defualtModuleConfig);
+
+        for (Path path : paths) {
+            ModuleConfig defaultModuleConfig = new ModuleConfig();
+            defaultModuleConfig.setSourceRoot(path.toString());
+            defaultModuleConfig.setExcludePatterns(convertToSkippedFolders(GlobalSettings.getInstance().getServerConfig().getExcludedPaths()));
+            applicationsConfig.modules.add(defaultModuleConfig);
+        }
 
         return applicationsConfig;
     }
-
 }