Kinematic analysis of the cycling position is a determining factor in injury prevention and optimal performance. Fatigue caused by high volume training can alter the kinematics of the lower body and spinal structures, thus increasing the risk of chronic injury. However, very few studies have established relationships between fatigue and postural change, being these in 2D analysis or incremental intensity protocols. Therefore, this study aimed to perform a 3D kinematic analysis of pedaling technique in a stable power fatigue protocol 23 amateur cyclists (28.3 ± 8.4 years) participated in this study. For this purpose, 3D kinematics in hip, knee, ankle, and lumbar joints, and thorax and pelvis were collected at three separate times during the protocol. Kinematic differences at the beginning, middle, and end of the protocol were analyzed for all joints using one-dimensional statistical parametric mapping. Significant differences (p < 0.05) were found in all the joints studied, but not all of them occur in the same planes or the same phase of the cycle. Some of the changes produced, such as greater lumbar and thoracic flexion, greater thoracic and pelvic tilt, or greater hip adduction, could lead to chronic knee and lumbar injuries. Therefore, bike fitting protocols should be carried out in fatigue situations to detect risk factor situations.