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An approach for direct in-pore solid-phase ultrashort peptide synthesis on mesoporous films using the amino acids arginine, leucine, and glycine is presented. Although the number of grafted amino acids remains low, the ionic mesopore accessibility can be gradually adjusted. The addition of arginine in up to five reaction cycles leads to a progressive increase in positive mesopore charge density, which gradually increases the anionic mesopore accessibility at acidic pH. At basic pH, the remaining silanol groups at the pore wall still dominate counter-charged cation mesopore accessibility. Thus, specific peptide sequence design is demonstrated to be a sensitive tool for molecular transport control in nanoscale pores. Overall, the direct in-pore solid-phase ultrashort peptide synthesis on mesoporous films using the sequences of different amino acids opens up exciting opportunities for the development of innovative materials with precisely tailored properties and functions based on specific peptide sequence design.