Spontaneous changes of movement patterns may allow to elucidate which criteria influence movement pattern preferences. However, the factors explaining the sit-stand transition in cycling are unclear. This study investigated if biomechanical and/or muscle activation cost functions could predict the power at which the spontaneous sit-stand transition occurs. Twenty-five participants performed an incremental test leading to the sit-to-stand transition, and subsequent randomized pedaling trials at 20 to 120% of the transition power in seated and standing position. A Moment Cost Function based on lower limbs net joint moments and two Electromyographic Cost Functions based on EMG data were defined. All cost functions increased with increasing crank power (p < 0.001) but at different rates in the seated and standing positions. They had lower values in the seated position below the transition power and lower values in the standing position above the transition power (p < 0.05). These results suggest that spontaneous change of position observed in cycling with increasing crank power represents an optimal choice to minimize muscular efforts. These results support the use of simple cost functions to define optimal settings in cycling and to assess the cost of cycling during short-term efforts.