Previous studies showed that feeding carbohydrate sources with different NSC profiles (e.g., starch vs. sucrose) and rates of ruminal degradation altered the milk fatty acids (FA) profile in dairy cows. This study evaluated the impact of corn meal (CM) or liquid molasses (MOL) on the milk FA profile of organically certified Jersey cows fed herbage-based diets. Ten multiparous (107 DIM) and 10 primiparous (131 DIM) lactating cows were blocked by parity, DIM, and milk yield and randomly assigned to 1 of 2 dietary treatments: CM or MOL. Diets were formulated to contain (DM basis): 74% herbage, 12% grass-legume mix hay, 12% CM or MOL, and 2% minerals and vitamins premix. The study lasted 110 d (June to September). Cows had access to pasture with mixed botanical composition (41.2% grass and 20% legume) for approximately 16 h daily in a strip grazing management system and were milked twice daily. Milk samples were collected monthly for 4 consecutive milkings, pooled by cow/period, and analyzed for milk FA using GLC. Herbage averaged (DM basis) 18.5% CP and 56.3% NDF, and 20% linoleic acid and 41.5% α-linolenic acid (% total FA). Milk FA was expressed as % total milk FA. Milk proportions of most saturated and unsaturated FA were affected by month, which are explained by variation in herbage botanical and FA composition, and milk yield. The milk proportion of total saturated FA was highest in cows fed MOL (71.8 vs. 71%). Milk proportions of α-linolenic acid (0.88 vs. 0.77%), trans-10,cis-12 CLA (0.090 vs. 0.078%), and PUFA (4.57 vs. 4.43%) were highest in cows fed MOL. Conversely, milk linoleic acid (1.12 vs. 1.72%), trans-10 18:1 (0.16 vs. 0.19%), trans-11 18:1 (2.62 vs. 2.76%), cis-9,trans-11 CLA (0.83 vs. 0.87%), and MUFA (22.8 vs. 23.7%) were lowest with MOL. The proportion of n-3 FA was highest (1.19 vs. 1.03%), whereas that of n-6 FA (1.30 vs. 1.35%) was lowest in cows fed MOL. Supplementing herbage-based diets with energy sources containing different NSC profiles resulted in marked changes in milk FA composition.