The aim of this study was to investigate the correlation of δ²H and δ¹³C of bulk milk powder and milk powder fatty acids to their production region. A total of 46 milk powder samples from across New Zealand were collected and analyzed. Principal component analysis (PCA) showed that the δ²H and δ¹³C of four fatty acids (C4:0, C14:0, C16:0, C18:1) and bulk milk powder were found to be correlated with regional production area. Linear discriminant analysis (LDA) models were prepared using different combinations of bulk and fatty acid δ²H and δ¹³C. All models were effective in discriminating samples from the North and South Islands. The LDA model using just fatty acid δ²H and δ¹³C provided the best separation. Therefore, the isotopic composition of the aforementioned fatty acids can be utilized as a good biomarker in milk powder that conveys reliable isotopic information to track milk powders to their regional origin.