National Agriculture Research Systems (NARS) perform a unique context-specific role in agriculture research and development, impacting food security in developing countries. NARS contribute to crop improvement research by generating improved plant varieties adapted to diverse agro-ecological zones and preferences of target populations. They are responsible for addressing the demands for orphan crops economically, culturally, and nutritionally relevant to specific populations in developing countries. The Feed the Future Innovation Lab for Crop Improvement (ILCI) aims to support NARS in developing and implementing Tools, Technologies, and Methodologies (TTMs) that enhance the delivery of genetic gains in crops that advance economic growth, crop resilience, and nutritional development in target populations. The Tata-Cornell Institute for Agriculture and Nutrition (TCI) is part of a multidisciplinary team within ILCI, tasked with researching institutional components that contribute to the capability of NARS to implement innovative TTMs to achieve genetic gain. This paper outlines the methodologies and outcomes of the approach implemented by TCI to establish baseline metrics to assess the capacities of ILCI partner NARS. To develop the metrics, TCI undertook a robust research process, incorporating a systematic literature review, evaluation of existing tools to measure breeding program capacity, consultation with experts, implementation of the Delphi technique, and a pilot with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) crop improvement programs. The scarcity of institutional capacity literature confirms the need for the framework TCI created. Currently, standardized methodologies to assess crop improvement programs with limited resources to contract experts for program evaluation are inadequate, exposing the potential demand for a low- input assessment tool. The metrics will be implemented through a survey instrument to compare institutional level capacities at the start and end of the ILCI project. An index will be constructed from survey responses to simplify multivariate indicators and enable comparisons over time. The objective is to assess the impact of TTM adoption through the ILCI project on capacity indicators.