Prilling by ultrasonic jet break-up is an efficient process to produce perfectly spherical microparticles homogeneous in size. However, the material properties could affect the manufacturability and the final product properties especially with lipid-based excipients which often exhibit complex structural properties. This work presents the characterisation of six lipid-based excipients differing by their melting point and polymorphic behaviour which were used to produce microspheres using a pilot-scale prilling equipment. The experimental results were compared to theoretical calculations, especially the droplet solidification time which is a key-parameter for this process. This work highlighted that monotropic polymorphism of excipients and supercooling effect have a significant impact on process parameters which should be considered with care during formulation design.