diff --git a/src/libcamera/camera_sensor.cpp b/src/libcamera/camera_sensor.cpp
index 572a313a..6670dfb9 100644
--- a/src/libcamera/camera_sensor.cpp
+++ b/src/libcamera/camera_sensor.cpp
@@ -19,6 +19,8 @@
 
 #include <libcamera/base/utils.h>
 
+#include <libcamera/transform.h>
+
 #include "libcamera/internal/bayer_format.h"
 #include "libcamera/internal/camera_lens.h"
 #include "libcamera/internal/camera_sensor_properties.h"
@@ -108,18 +110,51 @@ int CameraSensor::init()
 		return ret;
 
 	/*
-	 * Clear any flips to be sure we get the "native" Bayer order. This is
-	 * harmless for sensors where the flips don't affect the Bayer order.
+	 * We want to get the native mbus codes for the sensor, without any flips.
+	 * We can't clear any flips here, so we have to read the current values
+	 * (if the flip controls exist), decide whether they actually modify any
+	 * output Bayer pattern, and finally undo their effect on the formats.
+	 *
+	 * First, check if the flip controls exist and if so read them.
 	 */
 	ControlList ctrls(subdev_->controls());
-	if (subdev_->controls().find(V4L2_CID_HFLIP) != subdev_->controls().end())
-		ctrls.set(V4L2_CID_HFLIP, 0);
-	if (subdev_->controls().find(V4L2_CID_VFLIP) != subdev_->controls().end())
-		ctrls.set(V4L2_CID_VFLIP, 0);
-	subdev_->setControls(&ctrls);
+	std::vector<uint32_t> flipCtrlIds;
+	bool hasHflip = subdev_->controls().find(V4L2_CID_HFLIP) != subdev_->controls().end();
+	bool hasVflip = subdev_->controls().find(V4L2_CID_VFLIP) != subdev_->controls().end();
+	if (hasHflip)
+		flipCtrlIds.push_back(V4L2_CID_HFLIP);
+	if (hasVflip)
+		flipCtrlIds.push_back(V4L2_CID_VFLIP);
+	ControlList flipCtrls = subdev_->getControls(flipCtrlIds);
+
+	/* Now construct a transform that would undo any flips. */
+	Transform transform = Transform::Identity;
+	if (hasHflip && flipCtrls.get(V4L2_CID_HFLIP).get<int>()) {
+		const struct v4l2_query_ext_ctrl *extCtrl = subdev_->controlInfo(V4L2_CID_HFLIP);
+		if (extCtrl->flags & V4L2_CTRL_FLAG_MODIFY_LAYOUT)
+			transform |= Transform::HFlip;
+	}
+	if (hasVflip && flipCtrls.get(V4L2_CID_VFLIP).get<int>()) {
+		const struct v4l2_query_ext_ctrl *extCtrl = subdev_->controlInfo(V4L2_CID_VFLIP);
+		if (extCtrl->flags & V4L2_CTRL_FLAG_MODIFY_LAYOUT)
+			transform |= Transform::VFlip;
+	}
+
+	/* Finally get the formats, and apply the transform to the mbus codes. */
+	auto formats = subdev_->formats(pad_);
+	for (const auto &format : formats) {
+		unsigned int mbusCode = format.first;
+		BayerFormat bayerFormat = BayerFormat::fromMbusCode(mbusCode);
+		bool valid = true;
+
+		if (bayerFormat.isValid())
+			mbusCode = bayerFormat.transform(transform).toMbusCode(valid);
+
+		if (valid)
+			formats_[mbusCode] = std::move(format.second);
+	}
 
 	/* Enumerate, sort and cache media bus codes and sizes. */
-	formats_ = subdev_->formats(pad_);
 	if (formats_.empty()) {
 		LOG(CameraSensor, Error) << "No image format found";
 		return -EINVAL;