To achieve the goals of energy security and climate change mitigation in Denmark and the EU, an expansion of national production of bioenergy crops is needed. Temporal and spatial variation of yields of willow and Miscanthus is not known for Denmark because of a limited number of field trial data. The semi-mechanistic crop model BioCro was used to simulate the production of both short-rotation coppice (SRC) willow and Miscanthus across Denmark. Predictions were made from high spatial resolution soil data and weather records across this area for 1990–2010. The potential average, rain-fed mean yield was 12.1 Mg DM ha −1  yr −1 for willow and 10.2 Mg DM ha −1  yr −1 for Miscanthus. Coefficient of variation as a measure for yield stability was poorest on the sandy soils of northern and western Jutland, and the year-to-year variation in yield was greatest on these soils. Willow was predicted to outyield Miscanthus on poor, sandy soils, whereas Miscanthus was higher yielding on clay-rich soils. The major driver of yield in both crops was variation in soil moisture, with radiation and precipitation exerting less influence. This is the first time these two major feedstocks for northern Europe have been compared within a single modeling framework and providing an important new tool for decision-making in selection of feedstocks for emerging bioenergy systems. © 2015 The Authors. Global Change Biology Bioenergy Published by John Wiley & Sons Ltd.