diff --git a/apps/api/src/api/tool_instances.py b/apps/api/src/api/tool_instances.py
index 109dfa3..bf661f9 100644
--- a/apps/api/src/api/tool_instances.py
+++ b/apps/api/src/api/tool_instances.py
@@ -747,8 +747,46 @@ services:
 """
             write_compose_file(instance_dir, compose_content)
 
+        elif tool_type.definition_type == "manifest":
+            # Manifest-based: generate compose from manifest definition
+            from src.models.tool_definition_manifest import ToolDefinitionManifest
+
+            manifest_def = await session.get(
+                ToolDefinitionManifest, tool_type.manifest_id
+            )
+            if not manifest_def:
+                raise HTTPException(
+                    status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+                    detail="Manifest definition not found for this tool type",
+                )
+
+            manifest = dict(manifest_def.manifest)
+            if manifest_def.base_definition_id:
+                base_def = await session.get(
+                    ToolDefinitionManifest, manifest_def.base_definition_id
+                )
+                if base_def:
+                    manifest = resolve_base(
+                        deep_merge(dict(base_def.manifest), manifest)
+                    )
+
+            image_tag = compute_image_tag(tool_type.name, manifest)
+
+            variables = {
+                "IMAGE_TAG": image_tag,
+                "INSTANCE_NAME": instance_name.lower(),
+                "INSTANCE_DIR": instance_dir,
+                "REPO_PATH": repo_path,
+                "SSH_PATH": "",
+                "TOOL_PORT": tool_port,
+                "EXTRA_ENV": {},
+                "EXTRA_VOLUMES": [],
+            }
+            compose_content = compile_compose(manifest, variables)
+            write_compose_file(instance_dir, compose_content)
+
         else:
-            # Render compose template
+            # Render compose template (legacy)
             variables = {
                 "REPO_PATH": repo_path,
                 "INSTANCE_NAME": instance_name,