The FDA’s reclassification of transvaginal mesh as high-risk has revitalized the use of autologous fascial grafts for stress urinary incontinence (SUI) and pelvic organ prolapse (POP). While rectus fascia and fascia lata provide biocompatible alternatives, they present distinct complications. Rectus fascia harvest complications include hernia (1.2–5%), infection (1–5%), nerve injury, seroma (10–15%), and hematoma. Prevention involves proper patient selection and meticulous closure. Fascia lata harvest results in muscle herniation (15–36%), nerve injury with paresthesia (19–53%), seroma (3–14%), with generally lower wound complication rates than rectus fascia. Management of complications ranges from conservative approaches to surgical intervention. Studies report that most symptoms are mild, with eventual resolution and limited impact on quality of life. Understanding these complications is essential for patient counseling and optimal outcomes during autologous graft procedures.