The Internet of Medical Things (IoMT) plays a vital role in healthcare systems to increase electronic devices’ accuracy, reliability, and productivity. This paper presents fast multiple zero-watermarking methods based on Multi-channel Fractional Legendre Fourier moments (MFrLFMs) for medical image security and copyright protection in IoMT applications without deforming the original medical images. The MFrLFMs are utilized due to their high accuracy, numerical stability, geometric invariances, and high resistance to various attacks. Based on the most significant features generated from MFrLFMs, after scrambling using a two-dimensional Discrete Henon Map, then XORed with binary scrambled watermark to construct owner share. The proposed watermarking method is implemented using a low-cost Raspberry Pi Linux microprocessor, which ensures the suitability of medical devices in the IoMT environment. We evaluated the robustness of the proposed algorithm against different geometric and common signal processing attacks using various medical images. The proposed method gives better BER, NC, and SSIM values than existing methods.