This work is focused on developing a self-calibration algorithm for an orientation estimation of cattle movements based on a quaternion Kalman filter. The accelerometer signals in the earth's frame provide more information to confirm that the cow is performing a jump to mount another cow. To obtain the measurements in the earth's frame, we propose a self-calibration method based on a strapdown inertial navigation system (SINS), which does not require intervention by the user once deployed in the field. The self-calibration algorithm uses a quaternion-based Kalman filter to predict the angular orientation with bias correction, and update it based on the measurements of accelerometers and magnetometers. The paper also depicts an alternate update to adjust the inclination using only the accelerometer measurements. We conducted experiments to compare the accuracy of the orientation estimation when the body moves similarly to cow mount movements. The comparison is between the proposed self-calibration algorithm with the IvenSense MPU9250 and Bosch BNO055 and the quaternion attitude estimation provided in the BNO055. The auto-calibrating algorithm presents a mean error of 0.149 rads with a mean consumption of 308.5 mW, and the Bosch algorithm shows an average error of 0.139 rads with a mean consumption of 307.5 mW. When we executed this algorithm in an MPU9250, the average error was 0.077 rads, and the mean consumption was 277.7 mW.