Introduction: The agricultural sector faces increasing pressure to contribute to the Sustainable Development Goals (SDGs) while simultaneously acting as a driver of global climate change. In response, agroecology amongst other approaches is gaining recognition as a holistic framework to transform food systems towards greater sustainability and resilience. Methods: To facilitate standardized assessment of agroecological performance, the Tool for Agroecology Performance Evaluation (TAPE) was developed by the UN Food and Agriculture Organization (FAO). While a greenhouse gas (GHG) emission score was originally envisioned within the TAPE framework, to date, no standardized implementation exists. Results: This study presents a first step toward operationalizing such a score by estimating livestock GHG emissions, specifically from enteric fermentation and manure management, using TAPE data collected from smallholder farms in Kenya's Nandi and Bomet counties. Emission factors (EFs) derived from local studies were applied to improve accuracy of the GHG emission score, achieving a level of specificity comparable to Intergovernmental Panel on Climate Change (IPCC) Tier II methods. TAPE results showed correlations between total livestock emissions as well as milk-based emission intensity (EI) of cattle and the agroecological indicators: Efficiency, Recycling, and Resilience. Discussion: The correlations varied in direction and magnitude, with the strongest relation found for Recycling and EI. Our findings demonstrate (1) the feasibility of integrating a GHG emission estimation into TAPE, and (2) highlight its potential as a tool for identifying synergies and tradeoffs between agroecological performance, emissions and emission intensities.