The choice of ligand is an important parameter in the synthesis of metal halide perovskites such as methylammonium lead bromide (MAPbBr3) perovskite nanocrystals (PNCs). In this work, phenylalanine (Phe) was demonstrated, for the first time, as a highly effective capping ligand for synthesizing MAPbBr3 PNCs when used in conjunction with (3-aminopropyl) triethoxysilane (APTES) and oleic acid (OA) or methylphosphoric acid (MPA). Ultraviolet–visible absorption and photoluminescence (PL) emission spectroscopy, powder X-ray diffraction, and Fourier transform infrared spectroscopy were used to investigate the optoelectronic, structural, and surface properties of the PNCs. The combined use of Phe, APTES, and OA or MPA is demonstrated to be highly successful in passivating PNCs for achieving both improved PL and enhanced stability. The enhanced passivation by Phe is attributed to the three functional groups in Phe that can stabilize surface defects related to Pb2+, CH3NH3 +, and Br– by mediating pH and hydrophobicity. Based on all the experimental results, a model is proposed to explain the passivation mechanism involving Phe in conjunction with other amine and acid ligands. This study demonstrates the effectiveness of multiligand passivation of perovskites involving amino acid as the capping ligand.