In cattle, greenhouse gas (GHG) emissions and nutrient balance are influenced by factors such as diet composition, intake, and digestibility. This study evaluated CH4 emissions and surpluses of crude protein, using five simulated scenarios of supplementation in small-scale dairy systems (SSDS). In addition, two pasture managements (cut-and-carry versus grazing) and two varieties of legumes (red clover vs. white clover) were considered. The diets were tested considering similar milk yield and chemical composition; CH4 emission was estimated using Tier-2 methodology from the Intergovernmental Panel on Climate Change (IPCC), and the data were analyzed in a completely randomized 5 × 2 × 2 factorial design. Differences (p < 0.05) were found in predicted CH4 emissions per kg of milk produced (g kg−1 FCM 3.5%). The lowest predicted CH4 emissions were found for S3 and S4 as well as for pastures containing white clover. Lower dietary surpluses of CP (p < 0.05) were observed for the control diet (1320 g CP/d), followed by S5 (1793 g CP/d), compared with S2 (2175 g CP/d), as well as in cut-and-carry management with red clover. A significant correlation (p < 0.001) was observed between dry matter intake and CH4 emissions (g−1 and per kg of milk produced). It is concluded that the environmental impact of formulating diets from local inputs (S3 and S4) can be reduced by making them more efficient in terms of methane kg−1 of milk in SSDS.