Fast, energy-efficient, and continuous manufacturing of nanoparticles (NPs) with controlled size and distribution in polymer matrices is challenging. Herein, a microwave-powered dual-injection continuous flow reactor is presented to prepare silver NP (AgNP)/polycaprolactone (PCL) nanocomposites (AgNP/PCL NCs). Ultrasmall spherical AgNPs (US-AgNPs, 1.86 ± 0.77 nm) can be manufactured in the PCL matrix in less than 3 min at ∼35 °C by applying 60 W microwave power and a combined flow rate of 1.25:1.25 mL/min (Pump1:Pump2). The effect of NP size and amount on the thermal, optical, and antimicrobial properties and the crystallinity of NCs are discussed. The NC crystallinity is independent of the NP's size and amount, while the NC film roughness is highly dependent on NP size. The antibacterial activity of the US-AgNPs-containing NC toward (∼98.2%), (∼98.2%), and (∼99.1%) is higher than big AgNP-containing NCs (82.3%, 85.7%, and 92.3%, respectively), signifying a strong NP size dependency instead of Ag concentration.