diff --git a/libraries/AP_NavEKF3/AP_NavEKF3_Control.cpp b/libraries/AP_NavEKF3/AP_NavEKF3_Control.cpp
index 51c894d107..245d6200f4 100644
--- a/libraries/AP_NavEKF3/AP_NavEKF3_Control.cpp
+++ b/libraries/AP_NavEKF3/AP_NavEKF3_Control.cpp
@@ -108,6 +108,7 @@ void NavEKF3_core::setWindMagStateLearningMode()
     if (!inhibitMagStates && setMagInhibit) {
         inhibitMagStates = true;
         updateStateIndexLim();
+        // variances will be reset in CovariancePrediction
     } else if (inhibitMagStates && !setMagInhibit) {
         inhibitMagStates = false;
         updateStateIndexLim();
@@ -164,6 +165,7 @@ void NavEKF3_core::setWindMagStateLearningMode()
     if (onGround) {
         finalInflightYawInit = false;
         finalInflightMagInit = false;
+        magFieldLearned = false;
     }
 
     updateStateIndexLim();
diff --git a/libraries/AP_NavEKF3/AP_NavEKF3_Measurements.cpp b/libraries/AP_NavEKF3/AP_NavEKF3_Measurements.cpp
index d4af4ae59a..7d6596bcb6 100644
--- a/libraries/AP_NavEKF3/AP_NavEKF3_Measurements.cpp
+++ b/libraries/AP_NavEKF3/AP_NavEKF3_Measurements.cpp
@@ -278,6 +278,8 @@ void NavEKF3_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;
         }
     }
@@ -339,6 +341,11 @@ void NavEKF3_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_NavEKF3/AP_NavEKF3_core.cpp b/libraries/AP_NavEKF3/AP_NavEKF3_core.cpp
index 75003f5364..b8024bc4ba 100644
--- a/libraries/AP_NavEKF3/AP_NavEKF3_core.cpp
+++ b/libraries/AP_NavEKF3/AP_NavEKF3_core.cpp
@@ -1022,12 +1022,28 @@ void NavEKF3_core::CovariancePrediction()
         }
     }
 
+    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];
+    }
+
     if (!inhibitMagStates) {
         float magEarthVar = sq(dt * constrain_float(frontend->_magEarthProcessNoise, 0.0f, 1.0f));
         float magBodyVar  = sq(dt * constrain_float(frontend->_magBodyProcessNoise, 0.0f, 1.0f));
         for (uint8_t i=6; i<=8; i++) processNoiseVariance[i] = magEarthVar;
         for (uint8_t i=9; i<=11; i++) processNoiseVariance[i] = magBodyVar;
     }
+    lastInhibitMagStates = inhibitMagStates;
 
     if (!inhibitWindStates) {
         float windVelVar  = sq(dt * constrain_float(frontend->_windVelProcessNoise, 0.0f, 1.0f) * (1.0f + constrain_float(frontend->_wndVarHgtRateScale, 0.0f, 1.0f) * fabsf(hgtRate)));
@@ -1727,9 +1743,6 @@ void NavEKF3_core::resetMagFieldStates()
     P[20][20] = P[18][18];
     P[21][21] = P[18][18];
 
-    // prevent reset of variances in ConstrainVariances()
-    inhibitMagStates = false;
-
     // record the fact we have initialised the magnetic field states
     recordMagReset();
 }
diff --git a/libraries/AP_NavEKF3/AP_NavEKF3_core.h b/libraries/AP_NavEKF3/AP_NavEKF3_core.h
index cf16036506..98f56bdb3d 100644
--- a/libraries/AP_NavEKF3/AP_NavEKF3_core.h
+++ b/libraries/AP_NavEKF3/AP_NavEKF3_core.h
@@ -1088,6 +1088,8 @@ private:
     float tasTestRatio;             // sum of squares of true airspeed innovation divided by fail threshold
     bool inhibitWindStates;         // true when wind states and covariances are to remain constant
     bool inhibitMagStates;          // true when magnetic field states are inactive
+    bool lastInhibitMagStates;      // previous inhibitMagStates
+    bool needMagBodyVarReset;       // we need to reset mag body variances at next CovariancePrediction
     bool inhibitDelVelBiasStates;   // true when IMU delta velocity bias states are inactive
     bool inhibitDelAngBiasStates;   // true when IMU delta angle bias states are inactive
     bool gpsNotAvailable;           // bool true when valid GPS data is not available