A new strategy has been developed using peptides with amino and carboxylic functional groups as passivating ligands to produce methyl ammonium lead bromide (CH3NH3PbBr3) perovskite nanocrystals (PNCs) with excellent optical properties. The well‐passivated PNCs can only be obtained when both amino and carboxylic groups are involved, and this is attributed to the protonation reaction between NH2 and COOH that is essential for successful passivation of the PNCs. To better understand this synergistic effect, peptides with different lengths have been studied and compared. Due to the polar nature of peptides, peptide‐passivated PNCs (denoted as PNCspeptide) aggregate and precipitate from nonpolar toluene solvent, resulting in a high product yield (≈44%). Furthermore, the size of PNCspeptide can be varied from ≈3.9 to 8.6 nm by adjusting the concentration of the peptide, resulting in tunable optical properties due to the quantum confinement effect. In addition, CsPbBr3 PNCs are also synthesized with peptides as capping ligands, further demonstrating the generality and versatility of this strategy, which is important for generating high quality PNCs for photonics applications including light‐emitting diodes, optical sensing, and imaging. Peptides with different lengths are used in the synthesis of perovskite nanocrystals (PNCs) as capping ligands. PNCspeptide with tunable size (≈3.9 to 8.6 nm), prepared by adjusting the concentration of the peptides, exhibit size‐dependent optical properties due to quantum confinement effect. Such PNCs with peptides conjugated on their surface have potential applications in biomedicine, including optical sensing and imaging.