diff --git a/src/modules/ekf2/EKF2.cpp b/src/modules/ekf2/EKF2.cpp
index 6e9c9bb540..445203e7a0 100644
--- a/src/modules/ekf2/EKF2.cpp
+++ b/src/modules/ekf2/EKF2.cpp
@@ -2179,7 +2179,12 @@ void EKF2::UpdateBaroSample(ekf2_timestamps_s &ekf2_timestamps)
 
 		_ekf.set_air_density(airdata.rho);
 
-		// Rate-limit baro data to reduce EKF fusion CPU load
+		// Accumulate baro samples and average before pushing to EKF at the
+		// configured fusion rate.  This preserves the noise reduction of the
+		// old publish-side averaging while fixing the rate-aliasing bug.
+		_baro_prefilter_sum += airdata.baro_alt_meter;
+		_baro_prefilter_count++;
+
 		const float baro_rate_hz = _param_ekf2_baro_rate.get();
 		const hrt_abstime baro_interval_us = (baro_rate_hz > 0.f)
 						     ? static_cast<hrt_abstime>(1e6f / baro_rate_hz)
@@ -2187,8 +2192,13 @@ void EKF2::UpdateBaroSample(ekf2_timestamps_s &ekf2_timestamps)
 
 		if (reset || (baro_interval_us == 0)
 		    || (airdata.timestamp_sample >= _last_baro_ekf_timestamp + baro_interval_us)) {
-			_ekf.setBaroData(baroSample{airdata.timestamp_sample, airdata.baro_alt_meter, reset});
+
+			const float baro_avg = _baro_prefilter_sum / _baro_prefilter_count;
+			_ekf.setBaroData(baroSample{airdata.timestamp_sample, baro_avg, reset});
 			_last_baro_ekf_timestamp = airdata.timestamp_sample;
+
+			_baro_prefilter_sum = 0.f;
+			_baro_prefilter_count = 0;
 		}
 
 		ekf2_timestamps.vehicle_air_data_timestamp_rel = (int16_t)((int64_t)airdata.timestamp / 100 -
@@ -2535,7 +2545,11 @@ void EKF2::UpdateMagSample(ekf2_timestamps_s &ekf2_timestamps)
 			_mag_cal = {};
 		}
 
-		// Rate-limit mag data to reduce EKF fusion CPU load (3-axis fusion is expensive)
+		// Accumulate mag samples and average before pushing to EKF at the
+		// configured fusion rate.
+		_mag_prefilter_sum += Vector3f{magnetometer.magnetometer_ga};
+		_mag_prefilter_count++;
+
 		const float mag_rate_hz = _param_ekf2_mag_rate.get();
 		const hrt_abstime mag_interval_us = (mag_rate_hz > 0.f)
 						    ? static_cast<hrt_abstime>(1e6f / mag_rate_hz)
@@ -2543,8 +2557,13 @@ void EKF2::UpdateMagSample(ekf2_timestamps_s &ekf2_timestamps)
 
 		if (reset || (mag_interval_us == 0)
 		    || (magnetometer.timestamp_sample >= _last_mag_ekf_timestamp + mag_interval_us)) {
-			_ekf.setMagData(magSample{magnetometer.timestamp_sample, Vector3f{magnetometer.magnetometer_ga}, reset});
+
+			const Vector3f mag_avg = _mag_prefilter_sum / _mag_prefilter_count;
+			_ekf.setMagData(magSample{magnetometer.timestamp_sample, mag_avg, reset});
 			_last_mag_ekf_timestamp = magnetometer.timestamp_sample;
+
+			_mag_prefilter_sum.zero();
+			_mag_prefilter_count = 0;
 		}
 
 		ekf2_timestamps.vehicle_magnetometer_timestamp_rel = (int16_t)((int64_t)magnetometer.timestamp / 100 -
diff --git a/src/modules/ekf2/EKF2.hpp b/src/modules/ekf2/EKF2.hpp
index 18de839293..108716feef 100644
--- a/src/modules/ekf2/EKF2.hpp
+++ b/src/modules/ekf2/EKF2.hpp
@@ -311,6 +311,11 @@ private:
 	hrt_abstime _status_mag_pub_last{0};
 	hrt_abstime _last_mag_ekf_timestamp{0};
 
+	// Prefilter accumulators: average samples between fusion intervals to
+	// preserve noise reduction without the aliasing of the old publish-side rate limiter
+	Vector3f _mag_prefilter_sum{};
+	int _mag_prefilter_count{0};
+
 	uORB::Subscription _magnetometer_sub{ORB_ID(vehicle_magnetometer)};
 
 	uORB::PublicationMulti<estimator_aid_source3d_s> _estimator_aid_src_mag_pub{ORB_ID(estimator_aid_src_mag)};
@@ -355,6 +360,9 @@ private:
 	hrt_abstime _status_baro_hgt_pub_last{0};
 	hrt_abstime _last_baro_ekf_timestamp{0};
 
+	float _baro_prefilter_sum{0.f};
+	int _baro_prefilter_count{0};
+
 	float _last_baro_bias_published{};
 
 	uORB::Subscription _airdata_sub{ORB_ID(vehicle_air_data)};