A system and a method of mitigating color discrepancies in three-dimensional (3D) printing systems may including a plurality of printing heads may include: printing one or more samples according to one or more sample parameters; obtaining a color offset vector from the one or more samples; receiving a model representing a 3D object, the model comprising a plurality of model printing points associated with respective color; analyzing the model in view of the obtained color offset vector to produce a calibrated data structure, adapted to mitigate color discrepancies; and printing the 3D object according to the calibrated data structure.