The compliance of crab shells traditionally used as a complex natural product for agricultural soil amendment with modern biofertilizers' quality and safety requirements was investigated. Shells waste from the Blue crab, Callinectes sapidus and the Green crab, Carcinus aestuarii were tested for macronutrients, heavy metals, bacteria content, and antimicrobial properties. Such information is crucial for further utilization of the biogenic powders for any composite formulation in added-value by-products. The calcium carbonate-rich hard tissue yield was 52.13% ± 0.015 (mean ± S.D.) and 64.71% ± 0.144 from the blue and green crabs, respectively. The contents of Pb, Ni, Zn, Cr (VI), and Cu were several orders of magnitude below the prescribed limit by EU biofertilizer legislation, with Fe, Mn (not prescribed), and As being the most abundant. The content of As and Cd from the material considered here was within limits. The shells contain no colony-forming units of Salmonella spp. and compliant levels of Escherichia coli; moreover, the shell micro-powder showed dose-dependent growth inhibition of Pseudomonas aeruginosa and Staphylococcus aureus. In summary, the waste crab shells present a complex natural product as plant biofertilizer following the circular economy concepts.