Microfluidics opens new avenues for materials engineering, as it enables scalable synthesis and provides highly controllable environments for reactions. Herein, we leverage microfluidics to engineer the properties of (bioactive) metal–phenolic network nanoparticles (MPN NPs), an emerging and highly modular nanoparticle platform for the incorporation and delivery of bioactive cargo. By varying the microfluidics operating parameters (flow rate ratio, total flow rate, temperature) and NP composition, we assemble MPN NPs, which consist of poly(ethylene glycol), biomacromolecules, metal ions, and polyphenols. Compared to MPN NPs prepared via bulk assembly, the microfluidics-assembled MPN NPs possess a broader tunable size range (i.e., ∼40–330 nm vs ∼45–220 nm for bulk-assembled NPs) and a higher (by ∼30%) protein loading. The bulk-assembled MPN NPs show pH-responsive protein release behavior (e.g., ∼50% at pH 7; ∼25% at pH 9; 48 h). Likewise, the MPN NPs prepared via microfluidics at a flow rate ratio of 1:1 display similar pH-responsive protein release behavior. For the microfluidics-assembled MPN NPs, protein release is also dependent on temperature (e.g., 30% at 4 °C, and ∼50% at 20 and 37 °C). Furthermore, assembly at a 1:1 flow rate ratio overall enables greater tunability of protein release profiles than that at higher flow rate ratios. While bulk-assembled NPs display a higher degree of cell association, NPs assembled via both strategies can be internalized by cells after 24 h. These findings provide new insights into engineering the properties of metal–organic materials via microfluidics, which is expected to advance their development and application.