Chia seed oil has a higher omega-3 fatty acids content than other seeds, but, these fatty acids are easily oxidized. Microencapsulation helps to preserve them during handling and storage. The objective of this study was to obtain and characterize taro starch hydrolysates modified by succinylation and phosphorylation using thermoplastic extrusion, in order to use them in the microencapsulation of chia oil. Microcapsules were prepared with the obtained starches, via spray drying, using different mixtures of starch phosphates, starch succinates and maltodextrins. The encapsulated chia oil contained 54.99% of omega-3 fatty acids. Oil stability was monitored during 28 storage days, in order to evaluate n-hexanal as an oxidation indicator compound, by using solid phase micro gas chromatography and mass spectrometry. The highest encapsulation efficiency (73.89%) was for microcapsules prepared with mixtures of succynilated waxy corn starch:maltodextrins (50:50) followed by microcapsules prepared with succynilated taro starch:maltodextrins (50:50) and succynilated taro starch (100%) with encapsulation efficiency of 61.28% and 61.53% respectively. For stability monitoring it was found a positive effect by adding maltodextrins; the microcapsules showing higher oxidation protection were those made with succynilated taro starch:maltodextrins (50:50). Modified taro starch is an alternative as wall material for microencapsulation of chia oil.