A high number of studies support the use of mesoporous silica nanoparticles (MSN) as carriers for drug delivery systems due to its high biocompatibility both in vitro and in vivo, its large surface area, controlled pore size and, more than this, its good excretion capacity from the body. In this work we attempt to establish the optimal encapsulation parameters of benzalkonium chloride (BZC) into MSN and further study its drug release. The influence of different parameters towards the drug loading in MSN such as pH, contact time and temperature were considered. The adsorption mechanism of the drug has been determined by using the equilibrium data. The modification process was proved using several methods such as Fourier transform-infrared (FT-IR), ultraviolet-visible (UV-VIS), X-ray photoelectron spectroscopy (XPS) and thermogravimetric analysis (TGA). Since MSN shows a lower drug release amount due to the agglomeration tendency, in order to increase MSN dispersion and drug release amount from MSN, two common biocompatible and biodegradable polymers were used as polymer matrix in which the MSN-BZC can be dispersed. The drug release profile of the MSN-BZC and of the synthesized hybrid materials were studied both in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF). Polymer-MSN-BZC hybrid materials exhibit a higher drug release percent than the pure MSN-BZC when a higher dispersion is achieved. The dispersion of MSN into the hybrid materials was pointed out in scanning electron microscope (SEM) images. The release mechanism was determined using four mathematic models including first-order, Higuchi, Korsmeyer–Peppas and Weibull.