The spindle assembly checkpoint complex (SAC) is essential for quality control during mitosis in yeast and animals. However, its function in plants is not well understood. Here we show that MAD1, an Arabidopsis SAC component, is involved in endopolyploidization and flowering time via genetic interaction with MOS1, a negative regulator of plant immunity. MOS1 is found to interact with MAD2, another SAC component, and promote flowering and inhibit endopolyploidization, but this function is antagonized by MAD1. Furthermore, MAD1 and MOS1 both interact with SUF4, a transcription factor regulating the expression of the flowering time gene FLC. These findings reveal MOS1, MAD1 and SUF4 as regulators of endopolyploidization and flowering time and suggest an involvement of cell cycle control in the timing of reproductive transition.