The present invention relates to an amino acid fertilizer composition prepared by treating animal by-products with acid, alkali, and a proteinase. More particularly, the present invention relates to an amino acid fertilizer composition that is prepared by treating animal by-products such as cowhide, pigskin, or cow bones, with acid and alkali to give crude collagen peptides and then degrading the crude collagen peptides with a collagen-specific proteinase produced in Bacillus sp. Iren-101, which is a Bacillus sp. variant.