We used a double-jet mixer to encapsulate water-soluble polyphenols, green tea extract (GTE), with calcium-based inorganic materials. The device mixed calcium chloride solutions with a solution of carbonate and phosphate in the presence of a GTE solution, and formed micro-particles which capture the GTE molecules. The micro-particles were analysed by liquid chromatography coupled to tandem mass spectroscopy to determine the encapsulation yield and loading of the different GTE components. We established correlations between (1) the efficiency of the GTE encapsulation and the composition of the mixed anion solutions and (2) the protonation degree of the ions and the molar ratio of calcium cations and carbonate/phosphate anions. An optimal and reproducible GTE loading of about 40% with an encapsulation yield of 65% was observed for a carbonate/phosphate molar composition of 4 : 1. In addition, our experimental results showed that the process is selective and favours the encapsulation of gallated species which form stronger complexes with calcium cations.