Rosaceae is a vital plant family that includes a great diversity of plant species. Plant endophytic fungi reportedly can biosynthesize medicinally active secondary metabolites, acting as novel sources of natural bioactive products. This review evaluates the prospective exploitation of Rosaceae-associated fungal endophytes as dependable sources of natural bioactive compounds. It provides a comprehensive overview of these endophytes' metabolites and biological functions. The data has been collected from the Web of Science and PubMed databases. Alkaloids, sterols, terpenoids, coumarins, isocoumarins, and anthraquinones are the major compounds isolated from endophytic fungi. They have shown notable biological activities, mainly antibacterial, antifungal, and cytotoxic. In addition, it has been revealed that they boost plants to produce active metabolites. Therefore, these endophytes can serve as consistent, reliable, and eco-friendly sources of natural bioactive molecules. They can be exploited for the commercial production of medicines.