Marine-derived biowaste increment is enormous, yet could be converted into valuable biomaterial, e.g., hydroxyapatite-based bioceramic. Bioceramic material possesses superiority in terms of thermal, chemical, and mechanical properties. Bioceramic material also has a high level of biocompatibility when projected into biological tissues. Tuning the porosity of bioceramic material could also provide benefits for bioseparation application, i.e., ultrafiltration ceramic membrane filtration for food and dairy separation processes. This work presents the investigation of hydroxyapatite conversion from crab-shells marine-based biowaste, by comparing three different methods, i.e., microwave, coprecipitation, and sol–gel. The dried crab-shells were milled and calcinated as calcium precursor, then synthesized into hydroxyapatite with the addition of phosphates precursors via microwave, coprecipitation, or sol–gel. The compound and elemental analysis, degree of crystallinity, and particle shape were compared. The chemical compounds and elements from three different methods were similar, yet the degree of crystallinity was different. Higher Ca/P ratio offer benefit in producing a bioceramic ultrafiltration membrane, due to low sintering temperature. The hydroxyapatite from coprecipitation and sol–gel methods showed a significant degree of crystallinity compared with that of the microwave route. However, due to the presence of Fe and Sr impurities, the secondary phase of Ca9FeH(PO4)7 was found in the sol–gel method. The secondary phase compound has high absorbance capacity, an advantage for bioceramic ultrafiltration membranes. Furthermore, the sol–gel method could produce a snake-like shape, compared to the oval shape of the coprecipitation route, another benefit to fabricate porous bioceramic for a membrane filter.