diff --git a/agent-bases/js.AGENTS.md b/agent-bases/js.AGENTS.md
index 003cd8a42..eabab4159 100644
--- a/agent-bases/js.AGENTS.md
+++ b/agent-bases/js.AGENTS.md
@@ -26,6 +26,7 @@ Important: Before you begin, fill in the `generatedBy` property in the meta sect
 - implement retry strategies with exponential backoff for failed requests
 - use proper concurrency settings (HTTP: 10-50, Browser: 1-5)
 - set sensible defaults in `.actor/input_schema.json` for all optional fields
+- explicitly reference the input schema from `.actor/actor.json` by adding `"input": "./input_schema.json"` — do not rely on auto-discovery, which is deprecated
 - set up output schema in `.actor/output_schema.json`
 - clean and validate data before pushing to dataset
 - use semantic CSS selectors and fallback strategies for missing elements
@@ -187,8 +188,8 @@ Ask first:
 ## Project Structure
 
 .actor/
-├── actor.json # Actor config: name, version, env vars, runtime settings
-├── input_schema.json # Input validation & Console form definition
+├── actor.json # Actor config: name, version, env vars, runtime settings, input schema reference
+├── input_schema.json # Input validation & Console form definition (referenced from actor.json via "input")
 └── output_schema.json # Specifies where an Actor stores its output
 src/
 └── main.js # Actor entry point and orchestrator
diff --git a/agent-bases/python.AGENTS.md b/agent-bases/python.AGENTS.md
index 1797ae695..974e9271a 100644
--- a/agent-bases/python.AGENTS.md
+++ b/agent-bases/python.AGENTS.md
@@ -26,6 +26,7 @@ Important: Before you begin, fill in the `generatedBy` property in the meta sect
 - implement retry strategies with exponential backoff for failed requests
 - use proper concurrency settings (HTTP: 10-50, Browser: 1-5)
 - set sensible defaults in `.actor/input_schema.json` for all optional fields
+- explicitly reference the input schema from `.actor/actor.json` by adding `"input": "./input_schema.json"` — do not rely on auto-discovery, which is deprecated
 - set up output schema in `.actor/output_schema.json`
 - clean and validate data before pushing to dataset
 - use semantic CSS selectors and fallback strategies for missing elements
@@ -189,8 +190,8 @@ Ask first:
 ## Project Structure
 
 .actor/
-├── actor.json # Actor config: name, version, env vars, runtime settings
-├── input_schema.json # Input validation & Console form definition
+├── actor.json # Actor config: name, version, env vars, runtime settings, input schema reference
+├── input_schema.json # Input validation & Console form definition (referenced from actor.json via "input")
 └── output_schema.json # Specifies where an Actor stores its output
 src/
 └── main.js # Actor entry point and orchestrator
diff --git a/agent-bases/ts.AGENTS.md b/agent-bases/ts.AGENTS.md
index de8e3e29f..3a363ff2b 100644
--- a/agent-bases/ts.AGENTS.md
+++ b/agent-bases/ts.AGENTS.md
@@ -26,6 +26,7 @@ Important: Before you begin, fill in the `generatedBy` property in the meta sect
 - implement retry strategies with exponential backoff for failed requests
 - use proper concurrency settings (HTTP: 10-50, Browser: 1-5)
 - set sensible defaults in `.actor/input_schema.json` for all optional fields
+- explicitly reference the input schema from `.actor/actor.json` by adding `"input": "./input_schema.json"` — do not rely on auto-discovery, which is deprecated
 - set up output schema in `.actor/output_schema.json`
 - clean and validate data before pushing to dataset
 - use semantic CSS selectors and fallback strategies for missing elements
@@ -190,8 +191,8 @@ Ask first:
 ## Project Structure
 
 .actor/
-├── actor.json # Actor config: name, version, env vars, runtime settings
-├── input_schema.json # Input validation & Console form definition
+├── actor.json # Actor config: name, version, env vars, runtime settings, input schema reference
+├── input_schema.json # Input validation & Console form definition (referenced from actor.json via "input")
 └── output_schema.json # Specifies where an Actor stores its output
 src/
 └── main.js # Actor entry point and orchestrator
diff --git a/templates/js-empty/.actor/actor.json b/templates/js-empty/.actor/actor.json
index 1fab06922..1e01b4e2b 100644
--- a/templates/js-empty/.actor/actor.json
+++ b/templates/js-empty/.actor/actor.json
@@ -10,5 +10,6 @@
         "templateId": "js-empty",
         "generatedBy": "<FILL-IN-MODEL>"
     },
+    "input": "./input_schema.json",
     "dockerfile": "../Dockerfile"
 }
diff --git a/templates/js-empty/.actor/input_schema.json b/templates/js-empty/.actor/input_schema.json
new file mode 100644
index 000000000..819dfbb1f
--- /dev/null
+++ b/templates/js-empty/.actor/input_schema.json
@@ -0,0 +1,15 @@
+{
+    "$schema": "https://apify.com/schemas/v1/input.ide.json",
+    "title": "Actor Input",
+    "type": "object",
+    "schemaVersion": 1,
+    "properties": {
+        "example": {
+            "title": "Example Field",
+            "type": "string",
+            "description": "Replace this with your actual input fields.",
+            "editor": "textfield"
+        }
+    },
+    "required": []
+}
diff --git a/templates/python-empty/.actor/actor.json b/templates/python-empty/.actor/actor.json
index aa2f0886b..67890d863 100644
--- a/templates/python-empty/.actor/actor.json
+++ b/templates/python-empty/.actor/actor.json
@@ -10,5 +10,6 @@
         "templateId": "python-empty",
         "generatedBy": "<FILL-IN-MODEL>"
     },
+    "input": "./input_schema.json",
     "dockerfile": "../Dockerfile"
 }
diff --git a/templates/python-empty/.actor/input_schema.json b/templates/python-empty/.actor/input_schema.json
new file mode 100644
index 000000000..819dfbb1f
--- /dev/null
+++ b/templates/python-empty/.actor/input_schema.json
@@ -0,0 +1,15 @@
+{
+    "$schema": "https://apify.com/schemas/v1/input.ide.json",
+    "title": "Actor Input",
+    "type": "object",
+    "schemaVersion": 1,
+    "properties": {
+        "example": {
+            "title": "Example Field",
+            "type": "string",
+            "description": "Replace this with your actual input fields.",
+            "editor": "textfield"
+        }
+    },
+    "required": []
+}
diff --git a/templates/ts-empty/.actor/actor.json b/templates/ts-empty/.actor/actor.json
index cbbe54510..1d00285f4 100644
--- a/templates/ts-empty/.actor/actor.json
+++ b/templates/ts-empty/.actor/actor.json
@@ -10,5 +10,6 @@
         "templateId": "ts-empty",
         "generatedBy": "<FILL-IN-MODEL>"
     },
+    "input": "./input_schema.json",
     "dockerfile": "../Dockerfile"
 }
diff --git a/templates/ts-empty/.actor/input_schema.json b/templates/ts-empty/.actor/input_schema.json
new file mode 100644
index 000000000..819dfbb1f
--- /dev/null
+++ b/templates/ts-empty/.actor/input_schema.json
@@ -0,0 +1,15 @@
+{
+    "$schema": "https://apify.com/schemas/v1/input.ide.json",
+    "title": "Actor Input",
+    "type": "object",
+    "schemaVersion": 1,
+    "properties": {
+        "example": {
+            "title": "Example Field",
+            "type": "string",
+            "description": "Replace this with your actual input fields.",
+            "editor": "textfield"
+        }
+    },
+    "required": []
+}