The objective of this study was to compare N balance, microbial N flow (MNF) estimated from purine derivatives (PD) urinary excretion, and its variation when estimated using purine bases:N ratios in liquid associated bacteria (LAB) from models reported in the literature (MNF - response models) or measured ratios in liquid and solid-associated bacterial (SAB) pellets (MNF-LAB+SAB), diet digestibility, and rumen fermentation variables in sheep and goats fed 3 different practical, quality diets to study interspecies differences concerning N use as accurately as possible. Four mature female Merino sheep and 4 mature female Granadina goats, each fitted with a ruminal cannula, were used in 3 × 3 Latin square design with an extra animal. Two experimental diets had a forage-to-concentrate ratio of 70:30 (DM basis) with alfalfa hay (ALC) or grass hay (GRC) as forage, and the third diet contained 70% concentrate and 30% alfalfa hay (CAL). All animals were fed the diets at a daily rate of 56 g/kg BW(0.75) to minimize feed selection. Digestibility of nutrients was similar (P = 0.16 to 0.88) in the 2 species, but some animal species × diet interactions (P = 0.01 to 0.04) were detected. There were small differences between the fermentation patterns of both animal species. Goats showed decreased VFA concentrations (P = 0.005) and butyrate proportions (P = 0.04), and greater acetate proportions (P = 0.02) compared with sheep, whereas N intake and percentage of N intake excreted in feces were similar in both species (P = 0.58 and 0.15, respectively), the percentage excreted via the urine was greater in goats compared with sheep (P < 0.001). As a consequence, sheep had greater (P < 0.001) N retention than goats (averaged across diets, 32.6% and 16.1% of N intake, respectively). There were no differences (P = 0.95) between animal species in total PD excretion, but goats showed a greater excretion of allantoin (P = 0.01) and decreased excretion of xanthine (P = 0.008) and hypoxanthine (P = 0.007) compared with sheep. In general, differences between sheep and goats were more pronounced for the medium-quality diet (GRC) compared with those of high-quality diet (ALC and CAL). The greater urinary losses in goats would indicate a greater contribution of goats to N environmental contamination compared with sheep.