Turfgrass research based on inoculations with commercial products containing nitrogen‐fixing endophytes as an alternative to synthetic nitrogen (N) fertilizers has yielded inconclusive results, indicating a lack of understanding of the colonization and stability of diazotrophic endophytes in turfgrasses. Potential factors influencing these results are turfgrass traditional management practices. In this study, we identified and compared endophytic diazotrophic communities and their associated soil counterparts using amplicon sequencing of the nitrogenase iron protein (nifH) of 36 surfaced sterilized CitraBlue St. Augustinegrass cultivar [Stenotaphrum secundatum (Walter) Kuntze] sprigs and 12 aggregated soil samples. Samples were collected from a CitraBlue cultivar mowed either at 5 or 10 cm, with and without thatch removal, and fertilized at 98, 195, or 293 kg N ha−1 year−1. The different communities of endophytic diazotrophs were correlated to turfgrass quality related parameters such as normalized difference vegetation index (NDVI), normalized difference red edge index (NDRE), N leaf content, and visual quality as affected by management practices. CitraBlue endophytic and soil diazotrophic communities were significantly different for alpha diversity (p < 0.0001) and beta diversity (p < 0.001). Both mowing height (p < 0.001) and N fertilization rate (p < 0.05) had a significant effect on the diversity of endophytic diazotrophs. According to the redundancy analysis, turfgrass quality related parameters explained 14.3% of the variance in the endophytic diazotrophic communities. Findings from this research demonstrate that the evaluated management practices alter the endophytic diazotrophic communities of CitraBlue.