This study examined enteric and excreta emissions from cattle and pigs with a focus on effects of changed feeding practices. We assessed the impact of a revision of the Austrian Greenhouse Gas and Air Pollutant Inventory (national method, NM), i.e., the implementation of the Tier2-method of the IPCC-2019 guidelines, to a more dynamic integration of past and present feeding practices. Cattle—in particular, dairy cows—had the highest contribution to enteric CH4 emissions and to nitrogen (Nex) and volatile-solid (VSex) excretion, independent of the assessment method (NM or IPCC-2019). These emissions as well as excreta quantities are directly associated with feeding. The most relevant changes from implementing IPCC-2019 were (i) reduced enteric CH4 over the entire time series and (ii) increased Nex and VSex, especially for the period from 1990 to 2005. Additionally, uncertainties in the emissions and excreta were analyzed and related to the quantities of protein consumed. From 1990 to 2020, favorable trends per unit of protein were shown due to increased performance and concomitantly reduced animal numbers. The changes were especially pronounced for CH4, Nex, and VSex from dairy cows (−40% to −46%) but also substantial for other cattle (−26% to −31%), breeding pigs (−12% to −28%), and partially growing-fattening pigs (−3% to −20%). Future mitigation potential may result from reduced dietary crude-protein content, especially in pigs, and the use of feed additives. Feed additives for ruminants with enteric CH4-mitigating effects showed a particularly high reduction potential for the total amount of greenhouse gases from the livestock sector.