Although the antimicrobial activity of the engineered nanoparticles (NPs) is well known, the biochemical mechanisms underlying this activity are not clearly understood. Therefore, four NPs with the highest global production, namely SiO2, TiO2, ZnO, and Ag, were synthesized and characterized. The synthesized SiO2, TiO2, ZnO, and Ag NPs exhibit an average size of 11.12, 13.4, 35, and 50 nm, respectively. The antimicrobial activity of the synthesized NPs against bacteria and fungi were also determined. NPs-mediated inhibition of two very important enzymes, namely urease and DNA polymerase, is also reported. The synthesized NPs especially Ag and ZnO show significant antimicrobial activity against bacteria and fungi including methicillin-resistant Staphylococcus aureus even at low concentration. The DNA polymerase activity was inhibited at a very low concentration range of 2–4 µg/ml, whereas the urease activity was inhibited at a high concentration range of 50–100 µg/ml. Based on their ability to inhibit the urease and DNA polymerase, NPs can be arranged in the following order: Ag > ZnO > SiO2 > TiO2 and Ag > SiO2 > ZnO > TiO2, respectively. As the synthesized NPs inhibit bacterial growth and suppress the activity of urease and DNA polymerase, the use of these NPs to control pathogens is proposed.