diff --git a/cortex/api_key_detector.py b/cortex/api_key_detector.py
index eebfd4a3..fb8535e5 100644
--- a/cortex/api_key_detector.py
+++ b/cortex/api_key_detector.py
@@ -7,21 +7,23 @@
 Detection order (highest priority first):
 1. CORTEX_PROVIDER=ollama environment variable (for explicit Ollama mode)
 2. API key environment variables: ANTHROPIC_API_KEY, OPENAI_API_KEY
-3. Cached key location (~/.cortex/.api_key_cache)
-4. Saved Ollama provider preference in ~/.cortex/.env (CORTEX_PROVIDER=ollama)
-5. API keys in ~/.cortex/.env
-6. ~/.config/anthropic/credentials.json (Claude CLI location)
-7. ~/.config/openai/credentials.json
-8. .env in current directory
+3. Encrypted storage (~/.cortex/environments/cortex.json) - secure Fernet-encrypted storage
+4. Cached key location (~/.cortex/.api_key_cache)
+5. Saved Ollama provider preference in ~/.cortex/.env (CORTEX_PROVIDER=ollama)
+6. API keys in ~/.cortex/.env
+7. ~/.config/anthropic/credentials.json (Claude CLI location)
+8. ~/.config/openai/credentials.json
+9. .env in current directory
 
 Implements caching to avoid repeated file checks, file locking for safe
-concurrent access, and supports manual entry with optional saving to
-~/.cortex/.env.
+concurrent access, encrypted storage for sensitive keys, and supports
+manual entry with optional saving.
 
 """
 
 import fcntl
 import json
+import logging
 import os
 import re
 from pathlib import Path
@@ -29,6 +31,8 @@
 
 from cortex.branding import console, cx_print
 
+logger = logging.getLogger(__name__)
+
 # Constants
 CORTEX_DIR = ".cortex"
 CORTEX_ENV_FILE = ".env"
@@ -74,6 +78,14 @@ def detect(self) -> tuple[bool, str | None, str | None, str | None]:
         """
         Auto-detect API key from common locations.
 
+        Detection order (highest priority first):
+        1. CORTEX_PROVIDER=ollama environment variable
+        2. API key environment variables (ANTHROPIC_API_KEY, OPENAI_API_KEY)
+        3. Encrypted storage (~/.cortex/environments/cortex.json)
+        4. Cached key location
+        5. Saved Ollama provider preference
+        6. File-based locations (.env files, credentials.json)
+
         Returns:
             Tuple of (found, key, provider, source)
             - found: True if key was found
@@ -90,6 +102,11 @@ def detect(self) -> tuple[bool, str | None, str | None, str | None]:
         if result:
             return result
 
+        # Check encrypted storage (secure storage from first-run wizard)
+        result = self._check_encrypted_storage()
+        if result:
+            return result
+
         # Check cached location
         result = self._check_cached_key()
         if result:
@@ -113,6 +130,34 @@ def _check_environment_api_keys(self) -> tuple[bool, str, str, str] | None:
                 return (True, value, provider, "environment")
         return None
 
+    def _check_encrypted_storage(self) -> tuple[bool, str, str, str] | None:
+        """Check for API keys in encrypted storage (~/.cortex/environments/cortex.json).
+
+        This is the secure storage location used by the first-run wizard.
+        Keys are stored encrypted using Fernet encryption.
+        """
+        try:
+            from cortex.env_manager import get_env_manager
+
+            env_mgr = get_env_manager()
+
+            # Check for API keys in encrypted storage
+            for env_var, provider in ENV_VAR_PROVIDERS.items():
+                value = env_mgr.get_variable(app="cortex", key=env_var, decrypt=True)
+                if value:
+                    # Set in environment for this session
+                    os.environ[env_var] = value
+                    logger.debug(f"Loaded {env_var} from encrypted storage")
+                    return (True, value, provider, "encrypted storage (~/.cortex/environments/)")
+        except ImportError:
+            # cryptography not installed, skip encrypted storage check
+            logger.debug("cryptography not installed, skipping encrypted storage check")
+        except Exception as e:
+            # Log but don't fail - other detection methods may work
+            logger.debug(f"Could not check encrypted storage: {e}")
+
+        return None
+
     def _check_saved_ollama_provider(self) -> tuple[bool, str, str, str] | None:
         """Check if Ollama was previously selected as the provider in config file."""
         env_file = Path.home() / CORTEX_DIR / CORTEX_ENV_FILE
diff --git a/cortex/first_run_wizard.py b/cortex/first_run_wizard.py
index 6c7d22f9..bf8ad5ac 100644
--- a/cortex/first_run_wizard.py
+++ b/cortex/first_run_wizard.py
@@ -19,8 +19,13 @@
 from pathlib import Path
 from typing import Any
 
+from cortex.env_manager import get_env_manager
+
 logger = logging.getLogger(__name__)
 
+# Application name for storing cortex API keys
+CORTEX_APP_NAME = "cortex"
+
 
 class WizardStep(Enum):
     """Steps in the first-run wizard."""
@@ -786,21 +791,42 @@ def _prompt(self, message: str, default: str = "") -> str:
             return default
 
     def _save_env_var(self, name: str, value: str):
-        """Save environment variable to shell config."""
-        shell = os.environ.get("SHELL", "/bin/bash")
-        shell_name = os.path.basename(shell)
-        config_file = self._get_shell_config(shell_name)
+        """Save environment variable securely using encrypted storage.
 
-        export_line = f'\nexport {name}="{value}"\n'  # nosec - intentional user config storage
+        API keys are stored encrypted in ~/.cortex/environments/cortex.json
+        using Fernet encryption. The encryption key is stored in
+        ~/.cortex/.env_key with restricted permissions (chmod 600).
+        """
+        # Set for current session regardless of storage success
+        os.environ[name] = value
 
         try:
-            with open(config_file, "a") as f:
-                f.write(export_line)
-
-            # Also set for current session
-            os.environ[name] = value
+            env_mgr = get_env_manager()
+
+            # Handle brand names correctly (e.g., "OpenAI" not "Openai")
+            provider_name_raw = name.replace("_API_KEY", "")
+            if provider_name_raw == "OPENAI":
+                provider_name_display = "OpenAI"
+            elif provider_name_raw == "ANTHROPIC":
+                provider_name_display = "Anthropic"
+            else:
+                provider_name_display = provider_name_raw.replace("_", " ").title()
+
+            env_mgr.set_variable(
+                app=CORTEX_APP_NAME,
+                key=name,
+                value=value,
+                encrypt=True,
+                description=f"API key for {provider_name_display}",
+            )
+            logger.info(f"Saved {name} to encrypted storage")
+        except ImportError:
+            logger.warning(
+                f"cryptography package not installed. {name} set for current session only. "
+                "Install cryptography for persistent encrypted storage: pip install cryptography"
+            )
         except Exception as e:
-            logger.warning(f"Could not save env var: {e}")
+            logger.warning(f"Could not save env var to encrypted storage: {e}")
 
 
 # Convenience functions