diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp b/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp
index 0be20f3033..501ff3261a 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_Measurements.cpp
@@ -293,24 +293,61 @@ void NavEKF2_core::readIMUData()
     imuSampleTime_ms = AP_HAL::millis();
 
     // use the nominated imu or primary if not available
+    uint8_t accel_active, gyro_active;
+
     if (ins.use_accel(imu_index)) {
-        readDeltaVelocity(imu_index, imuDataNew.delVel, imuDataNew.delVelDT);
-        accelPosOffset = ins.get_imu_pos_offset(imu_index);
+        accel_active = imu_index;
     } else {
-        readDeltaVelocity(ins.get_primary_accel(), imuDataNew.delVel, imuDataNew.delVelDT);
-        accelPosOffset = ins.get_imu_pos_offset(ins.get_primary_accel());
+        accel_active = ins.get_primary_accel();
     }
 
-    // Get delta angle data from primary gyro or primary if not available
     if (ins.use_gyro(imu_index)) {
-        readDeltaAngle(imu_index, imuDataNew.delAng, imuDataNew.delAngDT);
+        gyro_active = imu_index;
     } else {
-        readDeltaAngle(ins.get_primary_gyro(), imuDataNew.delAng, imuDataNew.delAngDT);
+        gyro_active = ins.get_primary_gyro();
     }
 
+    if (gyro_active != gyro_index_active) {
+        // we are switching active gyro at runtime. Copy over the
+        // biases we have learned from the previously inactive
+        // gyro. We don't re-init the bias uncertainty as it should
+        // have the same uncertainty as the previously active gyro
+        stateStruct.gyro_bias = inactiveBias[gyro_active].gyro_bias;
+        gyro_index_active = gyro_active;
+
+        // use the gyro scale factor we have previously used on this
+        // IMU (if any). We don't reset the variances as we don't want
+        // errors after switching to be mis-assigned to the gyro scale
+        // factor
+        stateStruct.gyro_scale = inactiveBias[gyro_active].gyro_scale;
+    }
+
+    if (accel_active != accel_index_active) {
+        // switch to the learned accel bias for this IMU
+        stateStruct.accel_zbias = inactiveBias[accel_active].accel_zbias;
+        accel_index_active = accel_active;
+    }
+
+    // update the inactive bias states
+    learnInactiveBiases();
+
+    readDeltaVelocity(accel_index_active, imuDataNew.delVel, imuDataNew.delVelDT);
+    accelPosOffset = ins.get_imu_pos_offset(accel_index_active);
+    imuDataNew.accel_index = accel_index_active;
+
+    // Get delta angle data from primary gyro or primary if not available
+    readDeltaAngle(gyro_index_active, imuDataNew.delAng, imuDataNew.delAngDT);
+    imuDataNew.gyro_index = gyro_index_active;
+
     // Get current time stamp
     imuDataNew.time_ms = imuSampleTime_ms;
 
+    // use the most recent IMU index for the downsampled IMU
+    // data. This isn't strictly correct if we switch IMUs between
+    // samples
+    imuDataDownSampledNew.gyro_index = imuDataNew.gyro_index;
+    imuDataDownSampledNew.accel_index = imuDataNew.accel_index;
+
     // Accumulate the measurement time interval for the delta velocity and angle data
     imuDataDownSampledNew.delAngDT += imuDataNew.delAngDT;
     imuDataDownSampledNew.delVelDT += imuDataNew.delVelDT;
@@ -357,6 +394,8 @@ void NavEKF2_core::readIMUData()
         imuDataDownSampledNew.delVel.zero();
         imuDataDownSampledNew.delAngDT = 0.0f;
         imuDataDownSampledNew.delVelDT = 0.0f;
+        imuDataDownSampledNew.gyro_index = gyro_index_active;
+        imuDataDownSampledNew.accel_index = accel_index_active;
         imuQuatDownSampleNew[0] = 1.0f;
         imuQuatDownSampleNew[3] = imuQuatDownSampleNew[2] = imuQuatDownSampleNew[1] = 0.0f;
 
@@ -380,8 +419,8 @@ void NavEKF2_core::readIMUData()
         // correct the extracted IMU data for sensor errors
         delAngCorrected = imuDataDelayed.delAng;
         delVelCorrected = imuDataDelayed.delVel;
-        correctDeltaAngle(delAngCorrected, imuDataDelayed.delAngDT);
-        correctDeltaVelocity(delVelCorrected, imuDataDelayed.delVelDT);
+        correctDeltaAngle(delAngCorrected, imuDataDelayed.delAngDT, imuDataDelayed.gyro_index);
+        correctDeltaVelocity(delVelCorrected, imuDataDelayed.delVelDT, imuDataDelayed.accel_index);
 
     } else {
         // we don't have new IMU data in the buffer so don't run filter updates on this time step
@@ -540,7 +579,7 @@ bool NavEKF2_core::readDeltaAngle(uint8_t ins_index, Vector3f &dAng, float &dAng
     if (ins_index < ins.get_gyro_count()) {
         ins.get_delta_angle(ins_index,dAng);
         frontend->logging.log_imu = true;
-        dAng_dt = MAX(ins.get_delta_angle_dt(imu_index),1.0e-4f);
+        dAng_dt = MAX(ins.get_delta_angle_dt(ins_index),1.0e-4f);
         dAng_dt = MIN(dAng_dt,1.0e-1f);
         return true;
     }
@@ -832,4 +871,71 @@ void NavEKF2_core::writeExtNavData(const Vector3f &sensOffset, const Vector3f &p
 
 }
 
+/*
+  update estimates of inactive bias states. This keeps inactive IMUs
+  as hot-spares so we can switch to them without causing a jump in the
+  error
+ */
+void NavEKF2_core::learnInactiveBiases(void)
+{
+    const AP_InertialSensor &ins = AP::ins();
+
+    // learn gyro biases
+    for (uint8_t i=0; i<INS_MAX_INSTANCES; i++) {
+        if (!ins.use_gyro(i)) {
+            // can't use this gyro
+            continue;
+        }
+        if (gyro_index_active == i) {
+            // use current estimates from main filter of gyro bias and scale
+            inactiveBias[i].gyro_bias = stateStruct.gyro_bias;
+            inactiveBias[i].gyro_scale = stateStruct.gyro_scale;
+        } else {
+            // get filtered gyro and use the difference between the
+            // corrected gyro on the active IMU and the inactive IMU
+            // to move the inactive bias towards the right value
+            Vector3f filtered_gyro_active = ins.get_gyro(gyro_index_active) - (stateStruct.gyro_bias/dtEkfAvg);
+            Vector3f filtered_gyro_inactive = ins.get_gyro(i) - (inactiveBias[i].gyro_bias/dtEkfAvg);
+            Vector3f error = filtered_gyro_active - filtered_gyro_inactive;
+
+            // prevent a single large error from contaminating bias estimate
+            const float bias_limit = radians(5);
+            error.x = constrain_float(error.x, -bias_limit, bias_limit);
+            error.y = constrain_float(error.y, -bias_limit, bias_limit);
+            error.z = constrain_float(error.z, -bias_limit, bias_limit);
+
+            // slowly bring the inactive gyro in line with the active gyro. This corrects a 5 deg/sec
+            // gyro bias error in around 1 minute
+            inactiveBias[i].gyro_bias -= error * (1.0e-4f * dtEkfAvg);
+        }
+    }
+
+    // learn accel biases
+    for (uint8_t i=0; i<INS_MAX_INSTANCES; i++) {
+        if (!ins.use_accel(i)) {
+            // can't use this accel
+            continue;
+        }
+        if (accel_index_active == i) {
+            // use current estimate from main filter
+            inactiveBias[i].accel_zbias = stateStruct.accel_zbias;
+        } else {
+            // get filtered accel and use the difference between the
+            // corrected accel on the active IMU and the inactive IMU
+            // to move the inactive bias towards the right value
+            float filtered_accel_active = ins.get_accel(accel_index_active).z - (stateStruct.accel_zbias/dtEkfAvg);
+            float filtered_accel_inactive = ins.get_accel(i).z - (inactiveBias[i].accel_zbias/dtEkfAvg);
+            float error = filtered_accel_active - filtered_accel_inactive;
+
+            // prevent a single large error from contaminating bias estimate
+            const float bias_limit = 1; // m/s/s
+            error = constrain_float(error, -bias_limit, bias_limit);
+
+            // slowly bring the inactive accel in line with the active accel
+            // this learns 0.5m/s/s bias in about 1 minute
+            inactiveBias[i].accel_zbias -= error * (1.0e-4f * dtEkfAvg);
+        }
+    }
+}
+
 #endif // HAL_CPU_CLASS
diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp b/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp
index 4644c82225..839921ebdd 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_core.cpp
@@ -49,6 +49,8 @@ bool NavEKF2_core::setup_core(NavEKF2 *_frontend, uint8_t _imu_index, uint8_t _c
 {
     frontend = _frontend;
     imu_index = _imu_index;
+    gyro_index_active = _imu_index;
+    accel_index_active = _imu_index;
     core_index = _core_index;
     _ahrs = frontend->_ahrs;
 
@@ -378,7 +380,7 @@ bool NavEKF2_core::InitialiseFilterBootstrap(void)
     Vector3f initAccVec;
 
     // TODO we should average accel readings over several cycles
-    initAccVec = ins.get_accel(imu_index);
+    initAccVec = ins.get_accel(accel_index_active);
 
     // read the magnetometer data
     readMagData();
@@ -434,6 +436,15 @@ bool NavEKF2_core::InitialiseFilterBootstrap(void)
     // set to true now that states have be initialised
     statesInitialised = true;
 
+    // reset inactive biases
+    for (uint8_t i=0; i<INS_MAX_INSTANCES; i++) {
+        inactiveBias[i].gyro_bias.zero();
+        inactiveBias[i].accel_zbias = 0;
+        inactiveBias[i].gyro_scale.x = 1;
+        inactiveBias[i].gyro_scale.y = 1;
+        inactiveBias[i].gyro_scale.z = 1;
+    }
+
     // we initially return false to wait for the IMU buffer to fill
     return false;
 }
@@ -553,17 +564,17 @@ void NavEKF2_core::UpdateFilter(bool predict)
 #endif
 }
 
-void NavEKF2_core::correctDeltaAngle(Vector3f &delAng, float delAngDT)
+void NavEKF2_core::correctDeltaAngle(Vector3f &delAng, float delAngDT, uint8_t gyro_index)
 {
     delAng.x = delAng.x * stateStruct.gyro_scale.x;
     delAng.y = delAng.y * stateStruct.gyro_scale.y;
     delAng.z = delAng.z * stateStruct.gyro_scale.z;
-    delAng -= stateStruct.gyro_bias * (delAngDT / dtEkfAvg);
+    delAng -= inactiveBias[gyro_index].gyro_bias * (delAngDT / dtEkfAvg);
 }
 
-void NavEKF2_core::correctDeltaVelocity(Vector3f &delVel, float delVelDT)
+void NavEKF2_core::correctDeltaVelocity(Vector3f &delVel, float delVelDT, uint8_t accel_index)
 {
-    delVel.z -= stateStruct.accel_zbias * (delVelDT / dtEkfAvg);
+    delVel.z -= inactiveBias[accel_index].accel_zbias * (delVelDT / dtEkfAvg);
 }
 
 /*
@@ -646,8 +657,8 @@ void NavEKF2_core::calcOutputStates()
     // apply corrections to the IMU data
     Vector3f delAngNewCorrected = imuDataNew.delAng;
     Vector3f delVelNewCorrected = imuDataNew.delVel;
-    correctDeltaAngle(delAngNewCorrected, imuDataNew.delAngDT);
-    correctDeltaVelocity(delVelNewCorrected, imuDataNew.delVelDT);
+    correctDeltaAngle(delAngNewCorrected, imuDataNew.delAngDT, imuDataNew.gyro_index);
+    correctDeltaVelocity(delVelNewCorrected, imuDataNew.delVelDT, imuDataNew.accel_index);
 
     // apply corections to track EKF solution
     Vector3f delAng = delAngNewCorrected + delAngCorrection;
diff --git a/libraries/AP_NavEKF2/AP_NavEKF2_core.h b/libraries/AP_NavEKF2/AP_NavEKF2_core.h
index f17b95ef63..162f9a2a8f 100644
--- a/libraries/AP_NavEKF2/AP_NavEKF2_core.h
+++ b/libraries/AP_NavEKF2/AP_NavEKF2_core.h
@@ -30,6 +30,7 @@
 #include <stdio.h>
 #include <AP_Math/vectorN.h>
 #include <AP_NavEKF2/AP_NavEKF2_Buffer.h>
+#include <AP_InertialSensor/AP_InertialSensor.h>
 
 // GPS pre-flight check bit locations
 #define MASK_GPS_NSATS      (1<<0)
@@ -301,8 +302,9 @@ public:
     // publish output observer angular, velocity and position tracking error
     void getOutputTrackingError(Vector3f &error) const;
 
-    // get the IMU index
-    uint8_t getIMUIndex(void) const { return imu_index; }
+    // get the IMU index. For now we return the gyro index, as that is most
+    // critical for use by other subsystems.
+    uint8_t getIMUIndex(void) const { return gyro_index_active; }
 
     // get timing statistics structure
     void getTimingStatistics(struct ekf_timing &timing);
@@ -324,7 +326,9 @@ public:
 private:
     // Reference to the global EKF frontend for parameters
     NavEKF2 *frontend;
-    uint8_t imu_index;
+    uint8_t imu_index; // preferred IMU index
+    uint8_t gyro_index_active; // active gyro index (in case preferred fails)
+    uint8_t accel_index_active; // active accel index (in case preferred fails)
     uint8_t core_index;
     uint8_t imu_buffer_length;
 
@@ -409,6 +413,8 @@ private:
         float       delAngDT;       // 6
         float       delVelDT;       // 7
         uint32_t    time_ms;        // 8
+        uint8_t     gyro_index;
+        uint8_t     accel_index;
     };
 
     struct gps_elements {
@@ -468,6 +474,14 @@ private:
         bool            posReset;   // true when the position measurement has been reset
     };
 
+    // bias estimates for the IMUs that are enabled but not being used
+    // by this core.
+    struct {
+        Vector3f gyro_bias;
+        Vector3f gyro_scale;
+        float accel_zbias;
+    } inactiveBias[INS_MAX_INSTANCES];
+
     // update the navigation filter status
     void  updateFilterStatus(void);
 
@@ -574,12 +588,15 @@ private:
     bool readDeltaAngle(uint8_t ins_index, Vector3f &dAng, float &dAng_dt);
 
     // helper functions for correcting IMU data
-    void correctDeltaAngle(Vector3f &delAng, float delAngDT);
-    void correctDeltaVelocity(Vector3f &delVel, float delVelDT);
+    void correctDeltaAngle(Vector3f &delAng, float delAngDT, uint8_t gyro_index);
+    void correctDeltaVelocity(Vector3f &delVel, float delVelDT, uint8_t accel_index);
 
     // update IMU delta angle and delta velocity measurements
     void readIMUData();
 
+    // update estimate of inactive bias states
+    void learnInactiveBiases();
+
     // check for new valid GPS data and update stored measurement if available
     void readGpsData();