Flexible electronics is an emerging field in many applications ranging from in vivo biomedical devices to wearable smart systems. The capability of conforming to curved surfaces opens the door to add electronic components to miniaturized instruments, where size and weight are critical parameters. Given their prevalence on the sensors market, flexible magnetic sensors play a major role in this progress. For many high-performance applications, magnetic tunnel junctions (MTJs) have become the first choice, due to their high sensitivity, low power consumption etc. MTJs are also promising candidates for non-volatile next-generation data storage media and, hence, could become central components of wearable electronic devices. In this work, a generic low-cost regenerative batch fabrication process is utilized to transform rigid MTJs on a 500 µm silicon wafer substrate into 5 µm thin, mechanically flexible silicon devices, and ensuring optimal utilization of the whole substrate. This method maintains the outstanding magnetic properties, which are only obtained by deposition of the MTJ on smooth high-quality silicon wafers. The flexible MTJs are highly reliable and resistive to mechanical stress. Bending of the MTJ stacks with a diameter as small as 500 µm is possible without compromising their performance and an endurance of over 1000 cycles without fatigue has been demonstrated. The flexible MTJs are mounted onto the tip of a cardiac catheter with 2 mm in diameter without compromising their performance. This enables the detection of magnetic fields and the angle which they are applied at with a high sensitivity of 4.93%/Oe and a low power consumption of 0.15 μW, while adding only 8 and 5 μm to the weight and diameter of the catheter, respectively.