British-cross steers (n = 23; initial BW: 344 ± 33.9 kg) were used in a 3-period crossover design to evaluate the effect of protein supplementation to low-quality forage on ruminal methane (CH₄) and metabolic carbon dioxide (CO₂) emissions, forage intake, and microbial composition. Steers were individually given ad libitum access to low-quality bluestem hay (3.9% crude protein) and provided one of 3 supplements: (dry matter basis): no protein (CON), cottonseed meal (CSM; 0.29% of body weight (BW) daily) or dried distillers grains with solubles (DDGS; 0.41% of BW daily). Ruminal CH₄ and metabolic CO₂ fluxes were obtained 6.3 ± 1.6 times/steer daily using a GreenFeed unit (C-Lock Inc., Rapid City, SD). Microbial community structure of ruminal fluid collected using stomach tubes was determined using 16S rRNA based sequencing. Forage intake increased (P < 0.01) by 35.0% with protein supplementation; however, no difference (P = 0.14; SEM: 0.36) was observed between CSM (5.82 kg/d) and DDGS (5.50 kg/d). Flux of CO₂ (g/d) was greater (P < 0.01; SEM: 172.0) for steers fed CSM (5,520) and DDGS (5,453) than for steers fed CON (4,895). Steers supplemented with CSM (204.9) had greater (P < 0.01; SEM: 5.8) CH₄ emissions (g/d) than DDGS (189.2), both of which were greater (P < 0.01) than CON (174.1). Methane emissions, as a proportion of GE intake (Y_m), were lower (P < 0.01; SEM: 0.25) for DDGS (7.27%) and CSM steers (7.80%) than CON (10.10%). Principal coordinate analysis revealed shifts in microbial community structure with CON having greater abundance of specific operational taxonomic units (OTU) classified as Firmicutes and Streptococcus while CSM contained greater Bacteroidetes and Prevotella and DDGS steers had greater abundance of specific OTUs belonging to Clostridiales and Anaerobiviro. Results of this study suggests that the common practice of supplementing protein to cattle consuming low-quality forage increases overall gas emissions but yields beneficial decreases in greenhouse gas emissions per unit of intake and alters microbial community structure.