Excessive and frequent usage of synthetic fungicides has negative effects on the environment and human health. Biological control is one of the most efficient and environmentally responsible ways to manage plant diseases. In the present study, Bacillus velezensis strain B63, Bacillus subtilis subsp. Spizizenii strain TRC-20S and Serratia sp. Showed antifungal activities against Fusarium semitectum (synonym: Fusarium incarnatum), Macrophomina phaseolina, and Efibula tuberculata (MW063610) (synonym: Phanerochaete tuberculata). These fungi were isolated and purified from rotten geranium roots. M. phaseolina and F. semitectum were identified based on morphological and microscopic features. In addition, E. tuberculata was identified using the PCR technique. Bacillus velezensis strain B63 gave the best results in the terms of a decrease in plant mortality percentage and an increase in the geranium biometric parameters either under greenhouse or under field conditions. In addition, Bacillus velezensis strain B63 successfully increased the activity of defense-related enzymes, peroxidase (POD), and superoxide dismutase (SOD) and boosted the accumulation of total phenolic and flavonoid content in geranium leaves under field conditions. Also, the maximum essential oil yield with the highest eugenol content was recorded due to the application of B. velezensis and B. subtilis. Furthermore, anatomical analysis confirmed the positive role of biological control to induce resistance to root rot diseases through increasing root diameter, cortex thickness, vascular cylinder dimension, mean xylem vessel diameter, and xylem vessel number. Bacillus velezensis strain B63 possesses a broad expanse of antifungal and plant growth-promoting properties and can therefore play a vital role in boosting sustainable agriculture. This strain could be developed and applied in field experiments to improve plant growth and control root rot pathogens.