diff --git a/frontend/src/core/components/tools/automate/AutomationCreation.tsx b/frontend/src/core/components/tools/automate/AutomationCreation.tsx
index e71eb73e4..30c839e55 100644
--- a/frontend/src/core/components/tools/automate/AutomationCreation.tsx
+++ b/frontend/src/core/components/tools/automate/AutomationCreation.tsx
@@ -223,7 +223,7 @@ export default function AutomationCreation({ mode, existingAutomation, onBack, o
                 createdAt: existingAutomation?.createdAt || new Date().toISOString(),
                 updatedAt: new Date().toISOString()
               };
-              downloadFolderScanningConfig(tempAutomation);
+              downloadFolderScanningConfig(tempAutomation, toolRegistry);
             }}
             disabled={!canSaveAutomation()}
             variant="light"
diff --git a/frontend/src/core/components/tools/automate/AutomationSelection.tsx b/frontend/src/core/components/tools/automate/AutomationSelection.tsx
index 73dda0164..b7f600dda 100644
--- a/frontend/src/core/components/tools/automate/AutomationSelection.tsx
+++ b/frontend/src/core/components/tools/automate/AutomationSelection.tsx
@@ -59,7 +59,7 @@ export default function AutomationSelection({
             onClick={() => onRun(automation)}
             showMenu={true}
             onEdit={() => onEdit(automation)}
-            onExport={() => downloadFolderScanningConfig(automation)}
+            onExport={() => downloadFolderScanningConfig(automation, toolRegistry)}
             onDelete={() => onDelete(automation)}
             toolRegistry={toolRegistry}
           />
diff --git a/frontend/src/core/utils/automationConverter.ts b/frontend/src/core/utils/automationConverter.ts
index 1744f52f3..74b8e0a79 100644
--- a/frontend/src/core/utils/automationConverter.ts
+++ b/frontend/src/core/utils/automationConverter.ts
@@ -3,6 +3,8 @@
  */
 
 import { AutomationConfig } from '@app/types/automation';
+import { ToolRegistry } from '@app/data/toolsTaxonomy';
+import { ToolId } from '@app/types/toolId';
 
 /**
  * Pipeline configuration format used by folder scanning
@@ -24,18 +26,54 @@ interface FolderScanningPipeline {
 /**
  * Converts an AutomationConfig to a folder scanning pipeline configuration
  * @param automation The automation configuration to convert
+ * @param toolRegistry The tool registry to map operation types to endpoints
  * @returns Folder scanning pipeline configuration
  */
-export function convertToFolderScanningConfig(automation: AutomationConfig): FolderScanningPipeline {
+export function convertToFolderScanningConfig(
+  automation: AutomationConfig,
+  toolRegistry: Partial<ToolRegistry>
+): FolderScanningPipeline {
   return {
     name: automation.name,
-    pipeline: automation.operations.map(op => ({
-      operation: op.operation,
-      parameters: {
-        ...op.parameters,
-        fileInput: "automated"
+    pipeline: automation.operations.map(op => {
+      // Map operationType to full API endpoint path
+      const toolId = op.operation as ToolId;
+      const toolEntry = toolRegistry[toolId];
+      const endpointConfig = toolEntry?.operationConfig?.endpoint;
+
+      let endpoint: string | undefined;
+
+      if (typeof endpointConfig === 'string') {
+        endpoint = endpointConfig;
+      } else if (typeof endpointConfig === 'function') {
+        // For dynamic endpoints, call with the saved parameters
+        try {
+          endpoint = endpointConfig(op.parameters);
+        } catch (error) {
+          console.warn(
+            `Failed to resolve dynamic endpoint for operation "${op.operation}". ` +
+            `This may happen if the tool requires specific parameters. ` +
+            `Error: ${error}`
+          );
+        }
       }
-    })),
+
+      if (!endpoint) {
+        console.warn(
+          `No endpoint found for operation "${op.operation}". ` +
+          `This operation may fail in folder scanning. ` +
+          `Using operation type as fallback.`
+        );
+      }
+
+      return {
+        operation: endpoint || op.operation,
+        parameters: {
+          ...op.parameters,
+          fileInput: "automated"
+        }
+      };
+    }),
     _examples: {
       outputDir: "{outputFolder}/{folderName}",
       outputFileName: "{filename}-{pipelineName}-{date}-{time}"
@@ -48,9 +86,13 @@ export function convertToFolderScanningConfig(automation: AutomationConfig): Fol
 /**
  * Downloads a folder scanning configuration as a JSON file
  * @param automation The automation configuration to export
+ * @param toolRegistry The tool registry to map operation types to endpoints
  */
-export function downloadFolderScanningConfig(automation: AutomationConfig): void {
-  const config = convertToFolderScanningConfig(automation);
+export function downloadFolderScanningConfig(
+  automation: AutomationConfig,
+  toolRegistry: Partial<ToolRegistry>
+): void {
+  const config = convertToFolderScanningConfig(automation, toolRegistry);
   const json = JSON.stringify(config, null, 2);
   const blob = new Blob([json], { type: 'application/json' });
   const url = URL.createObjectURL(blob);