Midwest oak savannas contain some of the highest plant diversity in the United States and are among the rarest terrestrial ecosystems globally. Consequently, understanding diversity patterns within these ecosystems is important for setting management and restoration goals. This study aimed to understand the role of canopy cover and heterogeneity in canopy cover in influencing plant alpha and beta diversity within oak savanna ecosystems. This study took place in the black oak savannas of the Indiana Dunes along the southern shores of Lake Michigan in NW Indiana, USA. We sampled twenty-nine 1000 m² plots with gradients in canopy cover and canopy heterogeneity across the Indiana Dunes to examine the influence of canopy cover and canopy heterogeneity on plant diversity. Woody plant alpha diversity was highest in areas with a high canopy cover (>75%). C3 graminoids, C4 graminoids, and sedge alpha diversity were highest in low canopy cover areas (<25%). Forb and legume alpha diversity were highest with low to intermediate canopy cover (25–50% and 20–35%). Overall, plant alpha diversity was highest at intermediate canopy cover. High canopy heterogeneity was associated with high alpha diversity. There was no relationship between canopy cover or canopy heterogeneity with beta diversity. However, beta diversity was exceptionally high within all sites. An average canopy cover of 25–50% is the optimal cover for promoting high plant diversity across many functional groups. Still, low and high canopy cover sites are also important for maximizing diversity of some functional groups. Therefore, we recommend managing oak savannas for 25–50% canopy cover to maximize diversity, but where opportunities exist in large remnants of oak savanna, maintaining some areas with few trees and other areas with closed canopies can maximize diversity on a landscape scale.