We recently developed a novel approach for making oil-core silica-shell nanocapsules using designed bifunctional peptides (also called biomineralizing peptide surfactants) having both surface activity and biomineralization activity. Using the bifunctional peptides, oil-in-water nanoemulsion templates can be readily prepared, followed by the silicification directed exclusively onto the oil droplet surfaces and thus the formation of the silica shell. To explore their roles in the synthesis of silica nanocapsules, two bifunctional peptides, AM1 and SurSi, were systematically studied and compared. Peptide AM1, which was designed as a stimuli-responsive surfactant, demonstrated quick adsorption kinetics with a rapid decrease in the oil–water interfacial tension, thus resulting in the formation of nanoemulsions with a droplet size as small as 38 nm. Additionally, the nanoemulsions showed good stability over 4 weeks because of the formation of a histidine–Zn2+ interfacial network. In comparison, the SurSi peptide that was designed by modularizing an AM1-like surface-active module with a highly cationic biosilicification-active module was unable to effectively reduce the oil–water interfacial tension because of its high molecular charge at neutral pH. The slow adsorption resulted in the formation of less stable nanoemulsions with a larger size (60 nm) than that of AM1. Besides, both AM1 and SurSi were found to be able to induce biomimetic silica formation. SurSi produced well-dispersed and uniform silica nanospheres in the bulk solution, whereas AM1 generated only irregular silica aggregates. Consequently, well-defined silica nanocapsules were synthesized using SurSi nanoemulsion templates, whereas silica aggregates instead of nanocapsules predominated when templating AM1 nanoemulsions. This finding indicated that the capability of peptide surfactants to form isolated silica nanospheres might play a role in the successful fabrication of silica nanocapsules. This fundamental study provides insights into the design of bifunctional peptides for making silica nanocapsules.