This study investigated the effect of different collection methods on physical properties of pectin hydrogels in microfluidic synthetic approach. The pectin hydrogels were simply produced by the incorporation of calcium ions dissolved in continuous mineral oil. Then, different collection methods, pipetting, tubing, and settling, for harvesting pectin hydrogels were applied. The settling method showed most uniform and monodispersed hydrogels. In the case of settling, a coefficient of variation was 3.46 which was lower than pipetting method (18.60) and tubing method (14.76). Under the settling method, we could control the size of hydrogels, ranging from 30 μm to 180 μm, by simple manipulation of the viscosity of pectin and volumetric flow rate of dispersed and continuous phase. Finally, according to the characteristics of simple encapsulation of biological materials, we envision that the pectin hydrogels can be applied to drug delivery, food, and biocompatible materials.