Increasing bacterial resistance calls for the simultaneous delivery of multiple antibiotics. One strategy is to design a unique pharmaceutical carrier that is able to incorporate several drugs with different physico-chemical properties. This is highly challenging as it may require the development of compartmentalization approaches. Here we have prepared core–shell silica particles allowing for the dual delivery of gentamicin and rifamycin. The effect of silica particle surface functionalization on antibiotic sorption was first studied, enlightening the role of electrostatic and hydrophobic interactions. This in turn dictates the chemical conditions for shell deposition and further sorption of these antibiotics. In particular, the silica shell deposition was favored by the positively charged layer of gentamicin coating on the core particle surface. Shell modification by thiol groups finally allowed for rifamycin sorption. The antibacterial activity of the core–shell particles against Staphylococcus aureus and Pseudomonas aeruginosa demonstrated the dual release and action of the two antibiotics.