Ecological research is the central activity of the Konza Prairie. The site was established to provide a natural laboratory for the study of ecological patterns and processes in native tallgrass prairie ecosystems, and a protected field site for basic biological research. Kansas State University researchers and visiting scientists conduct field research on a wide spectrum of taxa and at levels of organization from the individual organism to landscape and global-scale processes. Ongoing research includes physiological ecology, population and community ecology of plants, insects, birds and mammals, aquatic ecology, ecosystem and landscape ecology, and grasslands restoration ecology. Studies of ecosystem dynamics emphasize productivity, nutrient cycling, and belowground processes. As of 2000, over 700 scientific articles and books were published based on research at Konza Prairie, and over 100 scientists have active research projects on site.

The three key natural processes that regulate and sustain the tallgrass prairie are periodic fire, ungulate grazing, and a variable continental climate. Thus, these processes are the focus of much of the long-term research. Replicated watershed-level experimental manipulations including fire and grazing are employed to study these ecological processes, with the effects of climate being investigated via measurements over long time scales and small-scale manipulations of precipitation patterns. Konza Prairie is divided into 60 watershed units (average size = 60 ha), each subjected to a specific combination of prescribed burning regime (burned at 1, 2, 3, 4, 10, or 20 year intervals, and burned in February, April, July, or November) and grazing treatment (grazed by bison, cattle, or ungrazed). The long-term prescribed burning treatments were initiated in 1972 and the bison grazing treatments were initiated in 1987. The herd of approximately 200 bison is managed to reflect a natural age structure and provides a year-long grazing regime resulting in approximately 25% removal of annual net primary productivity, a grazing intensity typical of natural sub-humid tall grasslands. The various combinations of bison, cattle, and ungrazed units allow large-scale replicated studies of the role of native grazers, comparison of effects of native and domestic ungulates, and effects of varying fire and grazing management regimes on tallgrass prairie ecosystems.