diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_Control.cpp b/libraries/AP_NavEKF2/AP_NavEKF2_Control.cpp
index 59137a5ac7..050141760d 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_Control.cpp
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_Control.cpp
@@ -105,6 +105,7 @@ void NavEKF2_core::setWindMagStateLearningMode()
     bool setMagInhibit = !magCalRequested || magCalDenied;
     if (!inhibitMagStates && setMagInhibit) {
         inhibitMagStates = true;
+        // variances will be reset in CovariancePrediction
     } else if (inhibitMagStates && !setMagInhibit) {
         inhibitMagStates = false;
         if (magFieldLearned) {
diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp b/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp
index a2242e4555..d3fa296cb0 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp
@@ -222,6 +222,9 @@ void NavEKF2_core::tryChangeCompass(void)
             magStateResetRequest = true;
             // declare the field unlearned so that the reset request will be obeyed
             magFieldLearned = false;
+
+            // reset body mag variances on next CovariancePrediction
+            needMagBodyVarReset = true;
             return;
         }
     }
@@ -285,6 +288,10 @@ void NavEKF2_core::readMagData()
             stateStruct.body_magfield.zero();
             // clear the measurement buffer
             storedMag.reset();
+            // reset body mag variances on next
+            // CovariancePrediction. This copes with possible errors
+            // in the new offsets
+            needMagBodyVarReset = true;
         }
         lastMagOffsets = nowMagOffsets;
         lastMagOffsetsValid = true;
diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp b/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp
index d033f40c27..65937d9538 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp
@@ -1082,6 +1082,23 @@ void NavEKF2_core::CovariancePrediction()
         zeroCols(P,22,23);
     }
 
+    if (!inhibitMagStates && lastInhibitMagStates) {
+        // when starting 3D fusion we want to reset body mag variances
+        needMagBodyVarReset = true;
+    }
+
+    if (needMagBodyVarReset) {
+        // reset body mag variances
+        needMagBodyVarReset = false;
+        zeroCols(P,19,21);
+        zeroRows(P,19,21);
+        P[19][19] = sq(frontend->_magNoise);
+        P[20][20] = P[19][19];
+        P[21][21] = P[19][19];
+    }
+
+    lastInhibitMagStates = inhibitMagStates;
+
     nextP[0][0] = daxNoise*SQ[3] + SPP[5]*(P[0][0]*SPP[5] - P[1][0]*SPP[4] + P[9][0]*SPP[22] + P[12][0]*SPP[18] + P[2][0]*(2*q1*SF[3] - 2*q2*SF[4] - 2*q3*SF[5] + 2*q0*SF[9])) - SPP[4]*(P[0][1]*SPP[5] - P[1][1]*SPP[4] + P[9][1]*SPP[22] + P[12][1]*SPP[18] + P[2][1]*(2*q1*SF[3] - 2*q2*SF[4] - 2*q3*SF[5] + 2*q0*SF[9])) + SPP[8]*(P[0][2]*SPP[5] + P[2][2]*SPP[8] + P[9][2]*SPP[22] + P[12][2]*SPP[18] - P[1][2]*(2*q0*SF[6] - 2*q3*SF[7] - 2*q1*SF[10] + 2*q2*SF[12])) + SPP[22]*(P[0][9]*SPP[5] - P[1][9]*SPP[4] + P[9][9]*SPP[22] + P[12][9]*SPP[18] + P[2][9]*(2*q1*SF[3] - 2*q2*SF[4] - 2*q3*SF[5] + 2*q0*SF[9])) + SPP[18]*(P[0][12]*SPP[5] - P[1][12]*SPP[4] + P[9][12]*SPP[22] + P[12][12]*SPP[18] + P[2][12]*(2*q1*SF[3] - 2*q2*SF[4] - 2*q3*SF[5] + 2*q0*SF[9]));
     nextP[0][1] = SPP[6]*(P[0][1]*SPP[5] - P[1][1]*SPP[4] + P[2][1]*SPP[8] + P[9][1]*SPP[22] + P[12][1]*SPP[18]) - SPP[2]*(P[0][0]*SPP[5] - P[1][0]*SPP[4] + P[2][0]*SPP[8] + P[9][0]*SPP[22] + P[12][0]*SPP[18]) + SPP[22]*(P[0][10]*SPP[5] - P[1][10]*SPP[4] + P[2][10]*SPP[8] + P[9][10]*SPP[22] + P[12][10]*SPP[18]) + SPP[17]*(P[0][13]*SPP[5] - P[1][13]*SPP[4] + P[2][13]*SPP[8] + P[9][13]*SPP[22] + P[12][13]*SPP[18]) - (2*q0*SF[5] - 2*q1*SF[4] - 2*q2*SF[3] + 2*q3*SF[9])*(P[0][2]*SPP[5] - P[1][2]*SPP[4] + P[2][2]*SPP[8] + P[9][2]*SPP[22] + P[12][2]*SPP[18]);
     nextP[1][1] = dayNoise*SQ[3] - SPP[2]*(P[1][0]*SPP[6] - P[0][0]*SPP[2] - P[2][0]*SPP[9] + P[10][0]*SPP[22] + P[13][0]*SPP[17]) + SPP[6]*(P[1][1]*SPP[6] - P[0][1]*SPP[2] - P[2][1]*SPP[9] + P[10][1]*SPP[22] + P[13][1]*SPP[17]) - SPP[9]*(P[1][2]*SPP[6] - P[0][2]*SPP[2] - P[2][2]*SPP[9] + P[10][2]*SPP[22] + P[13][2]*SPP[17]) + SPP[22]*(P[1][10]*SPP[6] - P[0][10]*SPP[2] - P[2][10]*SPP[9] + P[10][10]*SPP[22] + P[13][10]*SPP[17]) + SPP[17]*(P[1][13]*SPP[6] - P[0][13]*SPP[2] - P[2][13]*SPP[9] + P[10][13]*SPP[22] + P[13][13]*SPP[17]);
diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_core.h b/libraries/AP_NavEKF2/AP_NavEKF2_core.h
index e52d6c995d..7c16386557 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_core.h
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_core.h
@@ -946,6 +946,8 @@ private:
     float defaultAirSpeed;          // default equivalent airspeed in m/s to be used if the measurement is unavailable. Do not use if not positive.
     bool inhibitWindStates;         // true when wind states and covariances are to remain constant
     bool inhibitMagStates;          // true when magnetic field states and covariances are to remain constant
+    bool lastInhibitMagStates;      // previous inhibitMagStates
+    bool needMagBodyVarReset;       // we need to reset mag body variances at next CovariancePrediction
     bool gpsNotAvailable;           // bool true when valid GPS data is not available
     uint8_t last_gps_idx;           // sensor ID of the GPS receiver used for the last fusion or reset
     struct Location EKF_origin;     // LLH origin of the NED axis system