diff --git a/libraries/AP_Compass/AP_Compass_Calibration.cpp b/libraries/AP_Compass/AP_Compass_Calibration.cpp
index b9d73f2e33..b8da7070b3 100644
--- a/libraries/AP_Compass/AP_Compass_Calibration.cpp
+++ b/libraries/AP_Compass/AP_Compass_Calibration.cpp
@@ -50,9 +50,12 @@ Compass::start_calibration(uint8_t i, bool retry, bool autosave, float delay, bo
     if (!is_calibrating() && delay > 0.5f) {
         AP_Notify::events.initiated_compass_cal = 1;
     }
-    if (i == get_primary()) {
+    if (i == get_primary() && _state[i].external != 0) {
         _calibrator[i].set_tolerance(_calibration_threshold);
     } else {
+        // internal compasses or secondary compasses get twice the
+        // threshold. This is because internal compasses tend to be a
+        // lot noisier
         _calibrator[i].set_tolerance(_calibration_threshold*2);
     }
     _calibrator[i].start(retry, autosave, delay);