diff --git a/api/core/virtual_environment/factory.py b/api/core/sandbox/factory.py
similarity index 100%
rename from api/core/virtual_environment/factory.py
rename to api/core/sandbox/factory.py
diff --git a/api/core/virtual_environment/__base/command_future.py b/api/core/virtual_environment/__base/command_future.py
index 2c9cd5b6ea..88bef76054 100644
--- a/api/core/virtual_environment/__base/command_future.py
+++ b/api/core/virtual_environment/__base/command_future.py
@@ -47,6 +47,7 @@ class CommandFuture:
         self._done_event = threading.Event()
         self._lock = threading.Lock()
         self._result: CommandResult | None = None
+        self._exception: BaseException | None = None
         self._cancelled = False
         self._started = False
 
@@ -69,6 +70,9 @@ class CommandFuture:
         if self._cancelled:
             raise CommandCancelledError("Command was cancelled")
 
+        if self._exception is not None:
+            raise self._exception
+
         assert self._result is not None
         return self._result
 
@@ -127,16 +131,11 @@ class CommandFuture:
                     )
                     self._done_event.set()
 
-        except Exception:
+        except Exception as e:
             logger.exception("Command execution failed for pid %s", self._pid)
             with self._lock:
                 if not self._cancelled:
-                    self._result = CommandResult(
-                        stdout=bytes(stdout_buf),
-                        stderr=b"" if is_combined_stream else bytes(stderr_buf),
-                        exit_code=None,
-                        pid=self._pid,
-                    )
+                    self._exception = e
                     self._done_event.set()
         finally:
             self._close_transports()
diff --git a/api/core/virtual_environment/__base/initializer.py b/api/core/virtual_environment/__base/initializer.py
new file mode 100644
index 0000000000..dae03ae815
--- /dev/null
+++ b/api/core/virtual_environment/__base/initializer.py
@@ -0,0 +1,44 @@
+"""
+Sandbox initializer protocol for post-construction initialization.
+
+This module defines the interface for initializers that can perform
+setup tasks on newly created VirtualEnvironment instances.
+"""
+
+from abc import ABC, abstractmethod
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from core.virtual_environment.__base.virtual_environment import VirtualEnvironment
+
+
+class SandboxInitializer(ABC):
+    """
+    Abstract base class for sandbox post-construction initialization.
+
+    Initializers are called by VMFactory after a VirtualEnvironment is created.
+    They allow decoupling of environment creation from environment setup tasks
+    like uploading binaries, configuring tools, or setting up directories.
+
+    Example:
+        class MyInitializer(SandboxInitializer):
+            def initialize(self, env: VirtualEnvironment) -> None:
+                env.upload_file("/path/to/file", BytesIO(b"content"))
+    """
+
+    @abstractmethod
+    def initialize(self, env: "VirtualEnvironment") -> None:
+        """
+        Perform initialization on a newly created sandbox.
+
+        Called by VMFactory after VirtualEnvironment._construct_environment().
+        Implementations should be idempotent where possible.
+
+        Args:
+            env: The virtual environment to initialize.
+
+        Raises:
+            Exception: If initialization fails. The caller is responsible
+                for handling cleanup.
+        """
+        ...
diff --git a/api/core/virtual_environment/providers/e2b_sandbox.py b/api/core/virtual_environment/providers/e2b_sandbox.py
index 5f270ca6d0..98fec805df 100644
--- a/api/core/virtual_environment/providers/e2b_sandbox.py
+++ b/api/core/virtual_environment/providers/e2b_sandbox.py
@@ -250,6 +250,11 @@ class E2BEnvironment(VirtualEnvironment):
                 on_stdout=lambda data: stdout_stream_write_handler.write(data.encode()),
                 on_stderr=lambda data: stderr_stream_write_handler.write(data.encode()),
             )
+        except Exception as e:
+            # Capture exceptions and write to stderr stream so they can be retrieved via CommandFuture
+            # This prevents uncaught exceptions from being printed to console
+            error_msg = f"Command execution failed: {type(e).__name__}: {str(e)}\n"
+            stderr_stream_write_handler.write(error_msg.encode())
         finally:
             # Close the write handlers to signal EOF
             stdout_stream.close()
diff --git a/api/services/sandbox/sandbox_provider_service.py b/api/services/sandbox/sandbox_provider_service.py
index 9b6b116ada..76b75cd3e4 100644
--- a/api/services/sandbox/sandbox_provider_service.py
+++ b/api/services/sandbox/sandbox_provider_service.py
@@ -19,11 +19,11 @@ from sqlalchemy.orm import Session
 from configs import dify_config
 from constants import HIDDEN_VALUE
 from core.entities.provider_entities import BasicProviderConfig
+from core.sandbox.factory import VMFactory, VMType
 from core.tools.utils.system_encryption import (
     decrypt_system_params,
 )
 from core.virtual_environment.__base.virtual_environment import VirtualEnvironment
-from core.virtual_environment.factory import VMFactory, VMType
 from extensions.ext_database import db
 from models.sandbox import SandboxProvider, SandboxProviderSystemConfig
 from services.sandbox.encryption import create_sandbox_config_encrypter, masked_config
diff --git a/api/tests/unit_tests/core/virtual_environment/test_factory.py b/api/tests/unit_tests/core/virtual_environment/test_factory.py
index eed54cd80c..88e1f3f0a7 100644
--- a/api/tests/unit_tests/core/virtual_environment/test_factory.py
+++ b/api/tests/unit_tests/core/virtual_environment/test_factory.py
@@ -10,8 +10,8 @@ from unittest.mock import MagicMock, patch
 
 import pytest
 
+from core.sandbox.factory import VMFactory, VMType
 from core.virtual_environment.__base.virtual_environment import VirtualEnvironment
-from core.virtual_environment.factory import VMFactory, VMType
 
 
 class TestSandboxType: