In order to improve the quality of catfish bone flour, the sol-gel method was used to extract calcium. The purpose of the research was to compare calcium characterization, specifically chemical and physical quality based on discrepancy extraction methods. Completely Random Design was used as a factor with different calcium extraction, which were sol-gel method with agitation, a sol-gel treatment without agitation and the conventional way. Each treatment replicated in three folds. The results showed that the sol-gel process with agitation increased catfish bone flour quality (p<0.05), namely calcium (16.02%) and phosphor (5.13). Compared to the conventional method, the sol-gel way with and without agitation reduced particle size from from micro to sub-micro size by 174.67 µm to 3.82 and 5.12 µm respectively. The highest whiteness index (84.18) made micro calcium prepared by sol-gel method with agitation process as prospective for food fortification. Based on microscopic observation, catfish bone flour has calcite shape and stable structure which prospective used to substitute calcium loss in the bone.