The term “endophyte” refers to nonpathogenic microorganisms found within plants. These microorganisms are numerous, comprising several orders of both fungi and bacteria, and can operate as commensalistic or mutualistic symbionts with their hosts. Endophytes are distinguished by their ability to infiltrate plant tissues, persist, and interact with the host in a variety of ways. They enter plant tissues from within and can act as control agents or elicitors, causing resistance and alleviating the negative consequences of abiotic stress. They can improve plant fitness by lowering biotic and abiotic stress, encouraging the growth and development of plants, and decreasing agricultural output losses. This review examined the probable mechanisms of endophyte–host interactions. Endophytes create phytohormones that increase plant health and provide extra benefits such as nutrient intake, nitrogen fixation, and preservation under stress from abiotic as well as biotic settings. Some endophytes can actively protect their host plant from infections by secreting substances that kill or limit the growth of pathogenic microbes or by activating the plant immune response through the activation of the host plant’s natural signaling pathways. Endophytes inhibit infections via a variety of mechanisms, including mycoparasitism, competition, antibiosis, and plant defense induction, demonstrating their ability to control a wide spectrum of phytopathogenic organisms. They can also produce a wide range of bioactive compounds that are beneficial to plants. In this study, we detail the isolation techniques as well as various in vitro and in vivo studies on endophytes as biological control agents against pre- and postharvest illnesses. Furthermore, registration and regulatory strategies for endophytic biocontrol agents are discussed. Thus, isolating and identifying endophytic microorganisms from unstudied plants can lead to the discovery of novel species capable of producing chemicals of interest for application in disease control, induced resistance elicitors, and abiotic stress tolerance induction.