Volatile fatty acids (VFAs) are widely used across various industries, representing a significant global market. However, conventional petroleum-based VFAs production raises environmental concerns. Waste-derived VFAs offer a sustainable alternative, but the complexity of feed compositions poses significant challenges for efficient post-processing. This study analyzes the effects of operating conditions and coexisting compounds – ammonium/phosphorus-containing compounds and inorganic salts – on the performance of nanofiltration (NF) membranes for VFA recovery. It addresses a gap in the literature by providing a comprehensive analysis and theoretical insights into the combined effects of feed composition, membrane properties, and operating parameters on the semi-selective separation and concentration of VFAs from complex aqueous matrices. Three NF membranes with different molecular weight cut-offs and zeta potentials were tested under varying feed pH (5.5 and 9), applied pressure (10 bar, 20 bar, and 30 bar), and operating temperature (20 °C and 40 °C). Synthetic solutions simulating pretreated anaerobic digestion effluents were used in partial recirculation cross-flow NF experiments. Results demonstrate that ammonium/phosphorus-containing compounds reduced VFAs rejection by up to 10 %, while inorganic salts increased it by up to 15 %, both contributing to reduced permeate flux. The combined effects of membrane properties, feed composition, feed pH, and operating conditions impact the VFAs rejection mechanisms. At lower pH, size exclusion is the dominant mechanism, whereas at higher pH, electrostatic repulsion becomes more important, enhancing VFAs rejection but reducing permeate flux. Temperature and pressure had strong effects: higher pressure improved both solute rejection and flux, while higher temperature increased flux but reduced solute rejection. Feed pH 9, pressure 30 bar, and temperature 40 °C were identified as the most suitable operating parameters for maximizing VFAs rejection, minimizing the rejection of coexisting compounds, and maximizing permeate flux. Under these conditions, a retentate containing about 29 g/L of VFAs was recovered. This study offers insights for optimizing NF processes to improve waste-derived VFAs valorization, advancing sustainable resource recovery and supporting the circular bioeconomy.