Nearly half of all stars similar to our Sun are in binary or multiple systems(1), which may affect the evolution of the stars and their protoplanetary disks during their earliest stages. NGC1333-IRAS2A is a young, Class 0, low-mass protostellar system located in the Perseus molecular cloud. It is known to drive two bipolar outflows that are almost perpendicular to each other on the sky(3,4) and is resolved into binary components, VLA1 and VLA2, through long wavelength continuum observations(5). Here we report spatially and spectrally resolved observations of a range of molecular species. We compare these to detailed magnetohydrodynamic simulations: the comparisons show that inhomogeneous accretion onto the circumstellar disks occurs in episodic bursts, driving a wobbling jet. We conclude that binarity and multiplicity in general strongly affect the properties of the emerging stars, as well as the physical and chemical structures of the protoplanetary disks and therefore potentially any emerging planetary systems.