It was hypothesised that the inclusion of nitrate (NO3–) or cysteamine hydrochloride (CSH) in a protein deficient diet (4.8% crude protein; CP) would improve the productivity of sheep while reducing enteric methane (CH4) emissions. A complete randomised designed experiment was conducted with yearling Merino sheep (n = 24) consuming a protein-deficient wheaten chaff control diet (CON) alone or supplemented with 1.8% nitrate (NO3–; DM basis), 0.098% urea (Ur, DM basis) or 80 mg cysteamine hydrochloride/kg liveweight (CSH). Feed intake, CH4 emissions, volatile fatty acids (VFA), digesta kinetics and NO3–, nitrite (NO2–) and urea concentrations in plasma, saliva and urine samples were measured. There was no dietary effect on animal performance or digesta kinetics (P > 0.05), but adding NO3– to the CON diet reduced methane yield (MY) by 26% (P = 0.01). Nitrate supplementation increased blood MetHb, plasma NO3– and NO2– concentrations (P < 0.05), but there was no indication of NO2– toxicity. Overall, salivary NO3– concentration was greater than plasma NO3– (P < 0.05), indicating that NO3– was concentrated into saliva. Our results confirm the role of NO3– as an effective additive to reduce CH4 emissions, even in a highly protein-deficient diet and as a source of additional nitrogen (N) for microbial protein synthesis via N-recycling into saliva and the gut. The role of CSH as an additive in low quality diets for improving animal performance and reducing CH4 emissions is still unclear.