The co-evolution of peptide formation and membrane self-assembly is considered an essential step in the origin of life. However, more research is required on both processes, particularly on the interaction between prebiotic simple fatty-acid membranes and peptide synthesis. In this study, the sodium trimetaphosphate (P3 m)-activated peptide formation reaction of phenylalanine (Phe) in an alkaline decanoic acid-decanol vesicle system was systematically investigated. The experimental results showed that peptide formation could competitively occur with N-acyl amino acid (NAA) formation. NAA formation did not follow the traditional P3 m-activated peptide formation reaction involving the intermediate cyclic acylphosphoramidate (CAPA). Decanoic acid was activated by P3 m to form a mixed anhydride, which then reacted with an amino acid to form the amide NAA. As a kind of membrane-forming amphiphile, NAA can form vesicles independently and reduce the critical vesicle concentration of the fatty-acid vesicles. Moreover, 11 other representative amino acids, namely alanine (Ala), aspartic acid (Asp), glutamic acid (Glu), glycine (Gly), isoleucine (Ile), leucine (Leu), proline (Pro), serine (Ser), threonine (Thr), valine (Val), and arginine (Arg), were selected for investigation. All of them reacted with decanoic acid to form NAA via the activation effect of P3 m. The abovementioned mechanism involving P3 m-activated carboxylic acid has not been reported in the literature. Our experimental results indicate that the participation of decanoic acid in the P3 m activation-based peptide formation reaction system plays a significant role in the emergence of functionalized protocells. The P3 m activation effect can provide diversified raw membrane materials to form and stabilize protocell membranes; moreover, the small peptides, such as Phe-Leu, formed in the same reaction system can induce the amplification of primitive cells. This implies that synergistic symbiosis between membrane and peptide can be realized via the P3 m activation effect.