In response to the persistent challenge of heavy and noble metal environmental contamination, our research explores a new idea to capture silver through porous spherical silica nanostructures. The aim was realized using microwave radiation at varying power (P = 150 or 800 W) and exposure times (t = 60 or 150 s). It led to the development of a silica surface with enhanced metal-capture capacity. The microwave-assisted silica surface modification influences the notable changes within the carrier but also enforces the crystallization process of silver nanoparticles with different morphology, structure, and chemical composition. Microwave treatment can also stimulate the formation of core–shell bioactive Ag/Ag2CO3 heterojunctions. Due to the silver nanoparticles’ sphericity and silver carbonate’s presence, the modified nanocomposites exhibited heightened toxicity against common microorganisms, such as E. coli and S. epidermidis. Toxicological assessments, including minimum inhibitory concentration (MIC) and half-maximal inhibitory concentration (IC50) determinations, underscored the efficacy of the nanocomposites. This research represents a significant stride in addressing pollution challenges. It shows the potential of microwave-modified silicas in the fight against environmental contamination. Microwave engineering underscores a sophisticated approach to pollution remediation and emphasizes the pivotal role of nanotechnology in shaping sustainable solutions for environmental stewardship.