Intercropping is of increasing interest in temperate regions. This study assessed the influence of nitrogen (N) fertilization and sowing ratio on concentrations and uptake of micronutrients copper (Cu), iron (Fe), manganese (Mn), and zinc (Zn) in grain and residue of oat and pea in three substitutive intercrops on a fertile soil in eastern Austria. N increased grain concentrations of Cu and Zn in oat and pea but decreased the nutrient harvest indices especially for pea. Intercropping did not affect grain concentrations of oat but those of pea were increased in one year in intercrops with a lower pea share. Residue concentrations of Cu and Zn in oat were increased in intercrops with lower oat share. Pea residue concentrations of all four micronutrients were affected by intercropping. Slightly higher grain nutrient yields could be obtained for Mn and Zn in oat-dominated unfertilized intercrops, whereas the residue micronutrient yields were higher in all intercrops compared to pure stands because of generally higher nutrient concentrations in intercrops. Consequently, advantages of oat–pea intercrops for increasing micronutrient yield in grain were limited, but intercropping can be a strategy for increasing the micronutrient yield in residue that can be used for ruminant feeding.