diff --git a/flight/modules/StateEstimation/filterekf.c b/flight/modules/StateEstimation/filterekf.c
index 762b5e8ba..cdf8a7b99 100644
--- a/flight/modules/StateEstimation/filterekf.c
+++ b/flight/modules/StateEstimation/filterekf.c
@@ -233,9 +233,10 @@ static int32_t filter(stateFilter *self, stateEstimation *state)
         if (this->init_stage == 0) {
             // Reset the INS algorithm
             INSGPSInit();
-            INSSetMagVar((float[3]) { this->ekfConfiguration.R[EKFCONFIGURATION_R_MAGX],
-                                      this->ekfConfiguration.R[EKFCONFIGURATION_R_MAGY],
-                                      this->ekfConfiguration.R[EKFCONFIGURATION_R_MAGZ] }
+            // variance is measured in mGaus, but internally the EKF works with a normalized  vector. Scaling factor from old AHRS code (1000*1000)
+            INSSetMagVar((float[3]) { this->ekfConfiguration.R[EKFCONFIGURATION_R_MAGX] / 1e6f,
+                                      this->ekfConfiguration.R[EKFCONFIGURATION_R_MAGY] / 1e6f,
+                                      this->ekfConfiguration.R[EKFCONFIGURATION_R_MAGZ] / 1e6f }
                          );
             INSSetAccelVar((float[3]) { this->ekfConfiguration.Q[EKFCONFIGURATION_Q_ACCELX],
                                         this->ekfConfiguration.Q[EKFCONFIGURATION_Q_ACCELY],