diff --git a/Tools/autotest/arducopter.py b/Tools/autotest/arducopter.py
index 7e9a92a7f5..7fd8977752 100644
--- a/Tools/autotest/arducopter.py
+++ b/Tools/autotest/arducopter.py
@@ -2264,9 +2264,9 @@ class AutoTestCopter(AutoTest):
             self.set_parameter("EK3_SRC2_YAW", 6)   # External Nav
             self.set_parameter("RC7_OPTION", 80)    # RC aux switch 7 set to Viso Align
             self.set_parameter("RC8_OPTION", 90)    # RC aux switch 8 set to EKF source selector
-            self.reboot_sitl()
             self.set_parameter("EK2_ENABLE", 0)
             self.set_parameter("AHRS_EKF_TYPE", 3)
+            self.reboot_sitl()
 
             # switch to use GPS
             self.set_rc(8, 1000)