Microcapsules are applied in several sectors of industry when a physical barrier between the core material and the external environment is required. They protect their cargo and ultimately release it in a controlled way. In the present work, microcapsules with hydrogel-based shells are produced. Monodispersed microcapsules are formed by ionotropic gelation of gellan gum from monodispersed oil-in-water-in-oil (O/W/O) double emulsion templates obtained using glasscapillary microfluidic devices. An oil extraction step was added after the shell gelation process to enable the dispersion of the microcapsules in an aqueous medium. We report the operability window for the production of monodispersed microcapsules as a function of the flow rate of each fluid phase and the dimensions of the device. Microcapsules with mean diameters ranging from 95 to 260 um and a maximum coefficient of variation of 5 per cent were formed. The results show how to independently control the capsule diameter and shell thickness by varying the outer and middle phase flow rates. After that, we experimentally investigate the flow of monodispersed gellan gum microcapsules through a constricted capillary tube by measuring the evolution of the pressure difference and flow visualization. The maximum pressure difference and capsule deformation is obtained for capsules with different diameter and shell thickness. We map the conditions at which the capsule membrane ruptures during the flow, releasing its internal phase. Then, the gastro-resistance of gellan microcapsules is verified through an in vitro test that mimics the gastric and intestinal phases of digestion. Confocal fluorescence microscopy is used to track microcapsules integrity and we show that microcapsules cargo is released in the intestine mostly due to its pH. Finally, we demonstrate that it is possible to produce magnetic microcapsules with well controlled magnetic response by adding different amounts of ferrofluid to their core or shell. The microcapsules produced have great potential for different applications in food, biomedical, pharmaceutical and oil and gas industries.