Undesirable interactions between trace mineral elements and ruminal contents may occur during digestion when mineral salts are supplemented. Antimicrobial effects of copper sulfate (CuSO 4 ) may affect ruminal digestibility of nutrients when fed as a source of copper (Cu), while sodium selenite (Na 2 SeO 3 ) may be reduced in the rumen to less available forms of selenium (Se). Our objective was to evaluate if protection of CuSO 4 and Na 2 SeO 3 by lipid-microencapsulation would induce changes on ruminal microbial fermentation. We used 8 fermentors in a dual-flow continuous-culture system in a 4 × 4 duplicated Latin square with a 2 × 2 factorial arrangement of treatments. Factors were CuSO 4 protection (unprotected and protected by lipid-microencapsulation) and Na 2 SeO 3 protection (unprotected and protected by lipid-microencapsulation). Treatments consisted of supplementation with 15 mg/kg of Cu and 0.3 mg/kg of Se from either unprotected or protected (lipid-microencapsulated) sources, as follows: (1) Control (unprotected CuSO 4 + unprotected Na 2 SeO 3 ); (2) Cu-P (protected CuSO 4 + unprotected Na 2 SeO 3 ); (3) Se-P (unprotected CuSO 4 + protected Na 2 SeO 3 ); (4) (Cu+Se)-P (protected CuSO 4 + protected Na 2 SeO 3 ). All diets had the same nutrient composition and fermentors were fed 106 g of dry matter/d. Each experimental period was 10 d (7 d of adaptation and 3 d for sample collections). Daily pooled samples of effluents were analyzed for pH, NH 3 -N, nutrient digestibility, and flows (g/d) of total N, NH 3 -N, nonammonia N (NAN), bacterial N, dietary N, and bacterial efficiency. Kinetics of volatile fatty acids was analyzed in samples collected daily at 0, 1, 2, 4, 6, and 8 h after feeding. Main effects of Cu protection, Se protection, and their interaction were tested for all response variables. Kinetics data were analyzed as repeated measures. Protection of Cu decreased acetate molar proportion, increased butyrate proportion, and tended to decrease acetate: propionate ratio in samples of kinetics, but did not modify nutrient digestibility. Protection of Se tended to decrease NH 3 -N concentration, NH 3 -N flow, and CP digestibility; and to increase flows of nonammonia N and dietary N. Our results indicate that protection of CuSO 4 may increase butyrate concentration at expenses of acetate, while protection of Na 2 SeO 3 tended to reduce ruminal degradation of N. Further research is needed to determine the effects of lipid-microencapsulation on intestinal absorption, tissue distribution of Cu and Se, and animal performance.