A novel soybean variety, designated XB003A12 is provided. Also provided are the seeds of soybean variety XB003A12, cells from soybean variety XB003A12, plants of soybean XB003A12, and plant parts of soybean variety XB003A12. Methods provided include producing a soybean plant by crossing soybean variety XB003A12 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB003A12, methods for producing other soybean varieties or plant parts derived from soybean variety XB003A12, and methods of characterizing soybean variety XB003A12. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB003A12 are further provided.