This dataset supports the research paper “Cover crop effects on maize drought stress and yield” by Hunter et al. [1]. Data is provided on ecophysiological and yield measurements of maize grown following five functionally diverse cover crop treatments. The experiment was conducted in Pennsylvania, USA from 2013–2015 with organic management. Cover crops were planted in August after winter wheat harvest. Cover crops were terminated in late May of the following year, manure was applied, and both were incorporated with full inversion tillage prior to planting maize. The five cover crop treatments included a tilled fallow control, medium red clover, cereal rye, forage radish, and a 3-species mixture of medium red clover, cereal rye, and Austrian winter pea. Drought was imposed with rain exclusion shelters starting in early July. Results are provided for two subplots per cover crop treatment representing ambient and drought conditions. The dataset includes: 1) soil moisture in spring and during the maize growing season; 2) maize height, leaf chlorophyll content, leaf area index, stomatal conductance, and pre-dawn leaf xylem water potential; 3) maize yield and yield components including kernel biomass, total biomass, harvest index, number of plants per subplot, ears per plant, kernel mass, and kernel number per ear, per plant, and per subplot; 4) modeled season-long radiation interception and radiation use efficiency of biomass production; and 5) maize rooting density by depth in one year only. Data was collected in the field and lab using ecophysiological instruments (e.g., SPAD meter, ceptometer, porometer, and pressure chamber). Biomass samples were taken to determine yield. Data presented have been averaged to the subplot level (ambient and drought). This dataset can inform future research focused on using cover crops and other cultural practices to improve climate adaptation in cropping systems and also may be useful for meta-analyses.