Phosphorus (P) is an essential macronutrient in agriculture and has been listed as a critical raw material by the European Commission given its high demand and unequal distribution of phosphate rock reserves. In addition, crops can absorb a small part, and excess P fertilizers are washed away, resulting in eutrophication. Therefore, efforts must be made for the development of slow-release P fertilizer that can be absorbed effectively by crops. The objective of this study is to evaluate the slow release of P, converting insoluble phosphate to soluble forms. For this, grown cells of the acidophilic sulfur-oxidizing Acidithiobacillus (At.) thiooxidans were harvested to obtain a suspension with ~109 cell/mL, which were encapsulated in a matrix of alginate (3%) with CaCl2 (4%) together with elemental sulfur (0.4%) and Ca3(PO4)2 (0.25%). Beads with an average diameter of ~3 mm each were obtained and inoculated to a shake flask of 500 mL in triplicate; each containing 200 mL autotrophic basal salts with trace elements, and cultivated aerobically at 30 °C, shaken at 100 rpm for 21 days. Three initial pH were evaluated (2.0, 2.2, and 2.5). Samples were withdrawn at regular intervals to measure the soluble phosphate and sulfate. The results have confirmed the slow release of bioavailable phosphate by using At. thiooxidans encapsulated on the beads of alginate compared with experiments carried out with the suspension cells. This study opens new avenues for biotechnologies to dissolve insoluble sources of phosphate such as apatite to be applied as slow-release P fertilizer.