diff --git a/scripts/run_ardupilot_controller.sh b/scripts/run_ardupilot_controller.sh
index 7c9c32f..a13d560 100755
--- a/scripts/run_ardupilot_controller.sh
+++ b/scripts/run_ardupilot_controller.sh
@@ -14,12 +14,18 @@ set -e
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 PROJECT_DIR="$(dirname "$SCRIPT_DIR")"
 
+# Deactivate any existing virtual environment to avoid conflicts
+if [ -n "$VIRTUAL_ENV" ]; then
+    deactivate 2>/dev/null || true
+fi
+
 # Source ArduPilot environment
 if [ -f "$HOME/.ardupilot_env" ]; then
     source "$HOME/.ardupilot_env"
 fi
 
 # Activate ArduPilot venv (has empy and other dependencies)
+# This MUST be the active venv for sim_vehicle.py to work
 if [ -f "$HOME/venv-ardupilot/bin/activate" ]; then
     source "$HOME/venv-ardupilot/bin/activate"
 fi
@@ -36,9 +42,13 @@ if ! command -v sim_vehicle.py &> /dev/null; then
     exit 1
 fi
 
-# Activate virtual environment if exists
-if [ -f "$PROJECT_DIR/venv/bin/activate" ]; then
-    source "$PROJECT_DIR/venv/bin/activate"
+# Verify correct Python environment (ArduPilot venv should have empy)
+if ! python3 -c "import em" 2>/dev/null; then
+    echo "[WARN] empy not found in current Python environment"
+    echo "[INFO] Attempting to use ArduPilot venv..."
+    if [ -f "$HOME/venv-ardupilot/bin/activate" ]; then
+        source "$HOME/venv-ardupilot/bin/activate"
+    fi
 fi
 
 # Start SITL in background
diff --git a/setup/install_arch.sh b/setup/install_arch.sh
index ef2db3b..c397fc1 100755
--- a/setup/install_arch.sh
+++ b/setup/install_arch.sh
@@ -129,11 +129,17 @@ if [ -f "$HOME/.ardupilot_env" ]; then
     echo "[OK] ArduPilot environment"
 fi
 
+# Deactivate any existing venv to avoid conflicts
+if [ -n "$VIRTUAL_ENV" ]; then
+    deactivate 2>/dev/null || true
+fi
+
 # Activate ArduPilot venv (has empy and other dependencies)
+# This is preferred over project venv for ArduPilot compatibility
 if [ -f "$HOME/venv-ardupilot/bin/activate" ]; then
     source "$HOME/venv-ardupilot/bin/activate"
     echo "[OK] ArduPilot venv"
-# Fallback to project venv
+# Fallback to project venv only if ArduPilot not installed
 elif [ -f "$SCRIPT_DIR/venv/bin/activate" ]; then
     source "$SCRIPT_DIR/venv/bin/activate"
     echo "[OK] Python venv activated"
diff --git a/setup/install_ubuntu.sh b/setup/install_ubuntu.sh
index 32e286c..c6bb84f 100755
--- a/setup/install_ubuntu.sh
+++ b/setup/install_ubuntu.sh
@@ -183,11 +183,17 @@ if [ -f "$HOME/.ardupilot_env" ]; then
     echo "[OK] ArduPilot environment"
 fi
 
+# Deactivate any existing venv to avoid conflicts
+if [ -n "$VIRTUAL_ENV" ]; then
+    deactivate 2>/dev/null || true
+fi
+
 # Activate ArduPilot venv (has empy and other dependencies)
+# This is preferred over project venv for ArduPilot compatibility
 if [ -f "$HOME/venv-ardupilot/bin/activate" ]; then
     source "$HOME/venv-ardupilot/bin/activate"
     echo "[OK] ArduPilot venv"
-# Fallback to project venv
+# Fallback to project venv only if ArduPilot not installed
 elif [ -f "$SCRIPT_DIR/venv/bin/activate" ]; then
     source "$SCRIPT_DIR/venv/bin/activate"
     echo "[OK] Python venv"