The design and manufacture of innovative multifunctional materials possessing superior characteristics, quality and standards, rigorously required for future development of existing or emerging advanced technologies, is of great importance. These materials should have a very low degree of influence (or none) on the environmental and human health. Adjusting the properties of epoxy resins with organophosphorus compounds and silver-containing additives is key to the simultaneous improvement of the flame-resistant and antimicrobial properties of advanced epoxy-based materials. These environmentally friendly epoxy resin nanocomposites were manufactured using two additives, a reactive phosphorus-containing bisphenol derived from vanillin, namely, (4-(((4-hidroxyphenyl)amino)(6-oxido-6H-dibenzo[c,e][1,2]oxaphosphinin-6-yl)methyl)-2-methoxyphenyl) phenylphosphonate (BPH), designed as both cross-linking agent and a flame-retardant additive for epoxy resin; and additional silver-loaded zeolite L nanoparticles (Ze–Ag NPs) used as a doping additive to impart antimicrobial activity. The effect of BPH and Ze–Ag NPs content on the structural, morphological, thermal, flame resistance and antimicrobial characteristics of thermosetting epoxy nanocomposites was investigated. The structure and morphology of epoxy nanocomposites were investigated via FTIR spectroscopy and scanning electron microscopy (SEM). In general, the nanocomposites had a glassy and homogeneous morphology. The samples showed a single glass transition temperature in the range of 166–194 °C and an initiation decomposition temperature in the range of 332–399 °C. The introduction of Ze–Ag NPs in a concentration of 7–15 wt% provided antimicrobial activity to epoxy thermosets.