The objective was to investigate the effects of species (cow vs. goat) and of various dietary lipid supplements, known to modulate milk fat content, on selected metabolites and enzymes in milk and to explore their correlations with performance traits. Twelve Holstein cows and 12 Alpine goats, all multiparous and nonpregnant, and at 86 ± 24.9 and 61 ± 1.8 DIM, respectively, were fed a basal diet (45% forage + 55% concentrate) not supplemented (CTL) or supplemented with corn oil plus wheat starch [COS, 5% of diet dry matter (DM)], marine algae powder (MAP, 1.5% of diet DM), or hydrogenated palm oil (HPO, 3% of diet DM) in a replicated 4 × 4 Latin square design with 28-d experimental periods. Intake, milk production and composition, milk fatty acid profile, and plasma metabolite concentrations were previously reported. Concentrations of 9 milk metabolites [β-hydroxybutyrate (BHB), glucose, glucose-6-phosphate, isocitrate, choline, glutamate, urea, cholesterol, and free amino groups] and 2 milk enzyme activities (alkaline phosphatase and lactate dehydrogenase) were measured on d 24 of each experimental period. Dairy performance data showed marked species and diet effects on milk fat content. Irrespective of diet, cow milk was richer in alkaline phosphatase and glucose compared with goat milk (16 and 3 times more, respectively), whereas goat milk had greater urea and glucose-6-phosphate concentrations compared with cow milk (1.9 and 5.3 times more, respectively). In cows, COS decreased milk BHB and choline (-25 and -43%, respectively) compared with CTL, whereas no effects were observed in goats. The COS and MAP diets increased milk isocitrate compared with CTL in cows, but COS decreased isocitrate concentrations in goat milk. Milk choline was correlated with milk fat content in cows (Spearman r, rS = +0.73) and goats (rs = +0.58), and lactate dehydrogenase activity was correlated with milk somatic cell count (rs = +0.66) in cows but not in goats. We provide evidence of different milk metabolite responses according to species and diets. Metabolites and enzymes secreted in milk may be indicators of specificities of lipid metabolism among ruminant species and may contribute to a better understanding of mechanisms regulating milk fat secretion. Changes in the concentrations of some metabolites considered minor components of milk may be valuable diagnostic tools of mammary gland and animal metabolism as well as of milk processing characteristics.