Heavy metals and other organic pollutants burden the environment, and their removal or neutralization is still inadequate. The great potential for development in this area includes porous, spherical silica nanostructures with a well-developed active surface and open porosity. In this context, we modified the surface of silica spheres using a microwave field (variable power and exposure time) to increase the metal uptake potential and build stable bioactive Ag2O/Ag2CO3 heterojunctions. The results showed that the power of the microwave field (P = 150 or 700 W) had a more negligible effect on carrier modification than time (t = 60 or 150 s). The surface-activated and silver-loaded silica carrier features like morphology, structure, and chemical composition correlate with microbial and antioxidant enzyme activity. We demonstrated that the increased sphericity of silver nanoparticles enormously increased toxicity against E. coli, B. cereus, and S. epidermidis. Furthermore, such structures negatively affected the antioxidant defense system of E. coli, B. cereus, and S. epidermidis through the induction of oxidative stress, leading to cell death. The most robust effects were found for nanocomposites in which the carrier was treated for an extended period in a microwave field.