This work examines the use of stable isotopes and elemental composition for determining geographical origin and authenticity of cow milk from four geographical regions of Slovenian. Samples (277) were collected during summer and winter (2012 to 2014). It was possible to discriminate milk samples according to the year, season and production region using discriminant analysis (DA). The overall temporal prediction variability was 84.6% and 56.4% for regional differences. It was also possible to discriminate milk from three geographic regions, although Alpine samples overlap with Dinaric and Pannonian ones. Prediction ability was the highest for the Pannonian (82.1%) and lowest (26.9%) for the Alpine region. Pairwise comparison using OPLS-DA also displaying good regional predictability (≥0.77) with δ13Ccas values and Br content carrying the most variance. A model based on DD-SIMCA was also developed and applied to the control of Slovenian milk. The results revealed the mislabeling of three Slovenian milk products.