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Yields of crops must increase substantially over the coming decades to keep pace with global food demand driven by population and income growth. Ultimately global food production capacity will be limited by the amount of land and water resources available and suitable for crop production, and by biophysical limits on crop growth. Quantifying food production capacity on every hectare of current farmland in a consistent and transparent manner is needed to inform decisions on policy, research, development and investment that aim to affect future crop yield and land use, and to inform on-ground action by local farmers through their knowledge networks. Crop production capacity can be evaluated by estimating potential yield and water-limited yield levels as benchmarks for crop production under, respectively, irrigated and rainfed conditions. The differences between these theoretical yield levels and actual farmers’ yields define the yield gaps, and precise spatially explicit knowledge about these yield gaps is essential to guide sustainable intensification of agriculture. This paper reviews methods to estimate yield gaps, with a focus on the local-to-global relevance of outcomes. Empirical methods estimate yield potential from 90 to 95th percentiles of farmers’ yields, maximum yields from experiment stations, growers’ yield contests or boundary functions; these are compared with crop simulation of potential or water-limited yields. Comparisons utilize detailed data sets from western Kenya, Nebraska (USA) and Victoria (Australia). We then review global studies, often performed by non-agricultural scientists, aimed at yield and sometimes yield gap assessment and compare several studies in terms of outcomes for regions in Nebraska, Kenya and The Netherlands. Based on our review we recommend key components for a yield gap assessment that can be applied at local to global scales. Given lack of data for some regions, the protocol recommends use of a tiered approach with preferred use of crop growth simulation models applied to relatively homogenous climate zones for which measured weather data are available. Within such zones simulations are performed for the dominant soils and cropping systems considering current spatial distribution of crops. Need for accurate agronomic and current yield data together with calibrated and validated crop models and upscaling methods is emphasized. The bottom-up application of this global protocol allows verification of estimated yield gaps with on-farm data and experiments.