The dairy Nutrients Requirements of Cattle (NRC) was developed using data from purebred Holsteins and it might not accurately predict the performance of crossbred cattle. Our objectives were to evaluate the effects of two feeding levels (FLs) and three breed compositions (BCs) on nutrient intake, digestibility, performance, and methane (CH4) emissions of prepubertal dairy heifers. We used thirty-six heifers from three BCs: purebred Holstein (H), purebred Gyr (G), and F1 Holstein × Gyr (HG). Each BC had 12 animals and the experiment was designed as twelve incomplete three by three Latin squares, in a factorial arrangement three by two, with three BCs and two FLs (400 and 800 g/day). Total tract nutrient digestibility was determined using total fecal collection and DMI was individually measured. The data were analyzed using the PROC MIXED in SAS. Dry matter intake of all nutrients increased from the medium to high feeding level and the nutrients digestibility coefficients did differ among BCs. Achieved body weight gain in the medium FL treatment was greater than those predicted using the NRC, suggesting that crossbred and Gyr heifers have similar performance to Holsteins. Breed composition does not influence body weight gain of confined dairy heifers, but Holstein heifers fed a medium FL had higher feed efficiency and reduced CH4 emissions intensity.