The recognized biological properties of Ginkgo biloba extracts potentiate their utilization as an ingredient for functional foods. However, the digestive conditions can affect the chemical composition of the extracts and consequently their biological properties, which can lead to food safety problems. Thus, the impact of in vitro-simulated upper gastrointestinal tract digestion on the chemical composition and bioactivity of Ginkgo biloba leaf extract (GBE) was evaluated. The chemical composition of GBE was affected by in vitro digestion, but the antioxidant and antigenotoxic activities persisted. Therefore, G. biloba extract may be suitable for use as food additive and contribute to a healthy colon.