We demonstrated the generation of pectin hydrogel microparticles having complex shapes either by combining the phenomenon of gelation and water diffusion-induced self-assembly in microfluidic channels (on-chip) or by the deformation of the pregelled droplets outside the channels (off-chip) at a fluid-fluid interface. We proved that by tuning the mode of pectin cross-linking (CaCl2 vs CaCO3) and the degree of shrinking (water content in the dimethyl carbonate (DMC) organic continuous phase) we can control the shape of the final particle. Sphere, doughnut, oblate ellipsoid, or mushroom-type morphologies were thus produced, demonstrating the ability to control the formation of anisotropic biopolymer-based hydrogel microparticles using microfluidics. Shape changes were explained by the redistribution of calcium ions in combination with the local Peclet number experienced by the microdroplets during the on-chip process. Moreover, during the off-chip process, the interplay between elastic and viscous forces for microdroplets entering the CaCl2-DMC interface caused deformation of the pregelled droplets to occur and therefore resulted in the formation of microparticles with a mushroom-like morphology.