diff --git a/src/libcamera/pipeline/raspberrypi/raspberrypi.cpp b/src/libcamera/pipeline/raspberrypi/raspberrypi.cpp
index 49d7ff23..c1fb9666 100644
--- a/src/libcamera/pipeline/raspberrypi/raspberrypi.cpp
+++ b/src/libcamera/pipeline/raspberrypi/raspberrypi.cpp
@@ -1279,20 +1279,24 @@ int PipelineHandlerRPi::registerCamera(MediaDevice *unicam, MediaDevice *isp, Me
 	 * Thirdly, what is the "native" Bayer order, when no transforms are
 	 * applied?
 	 *
-	 * As part of answering the final question, we reset the camera to
-	 * no transform at all.
+	 * We note that the format list has already been populated with
+	 * whatever flips are currently set, so to answer the final question
+	 * we get the current Bayer order and undo the transform implied by
+	 * the current flip settings.
 	 */
 	const V4L2Subdevice *sensor = data->sensor_->device();
 	const struct v4l2_query_ext_ctrl *hflipCtrl = sensor->controlInfo(V4L2_CID_HFLIP);
+	Transform currentTransform = Transform::Identity;
 	if (hflipCtrl) {
 		/* We assume it will support vflips too... */
 		data->supportsFlips_ = true;
 		data->flipsAlterBayerOrder_ = hflipCtrl->flags & V4L2_CTRL_FLAG_MODIFY_LAYOUT;
 
-		ControlList ctrls(data->sensor_->controls());
-		ctrls.set(V4L2_CID_HFLIP, 0);
-		ctrls.set(V4L2_CID_VFLIP, 0);
-		data->setSensorControls(ctrls);
+		ControlList ctrls = data->sensor_->getControls({ V4L2_CID_HFLIP, V4L2_CID_VFLIP });
+		if (ctrls.get(V4L2_CID_HFLIP).get<int32_t>())
+			currentTransform ^= Transform::HFlip;
+		if (ctrls.get(V4L2_CID_VFLIP).get<int32_t>())
+			currentTransform ^= Transform::VFlip;
 	}
 
 	/* Look for a valid Bayer format. */
@@ -1307,7 +1311,10 @@ int PipelineHandlerRPi::registerCamera(MediaDevice *unicam, MediaDevice *isp, Me
 		LOG(RPI, Error) << "No Bayer format found";
 		return -EINVAL;
 	}
-	data->nativeBayerOrder_ = bayerFormat.order;
+	/* Applying the inverse transform will give us the native order. */
+	BayerFormat nativeBayerFormat = bayerFormat.transform(-currentTransform);
+	data->nativeBayerOrder_ = nativeBayerFormat.order;
+	LOG(RPI, Debug) << "Native Bayer format is " << nativeBayerFormat.toString();
 
 	/*
 	 * List the available streams an application may request. At present, we