The development of polymer-based nanoparticles to ferry siRNA continues to evolve. It is becoming increasingly apparent that gene silencing nanoparticles produced by conventional bulk manufacturing techniques often exhibit physicochemical heterogeneity within and between batches that can affect the biological performance. Here a new facile and robust "chip-free" method is presented, termed chip-free agitation-generated droplets (CAD) preparation, using chitosan-based gene silencing nanoparticles as an example. The CAD-prepared silencing particles, in comparison to the particles prepared by the conventional bulk protocol, exhibit lower surface charge (9 mV vs 21 mV at N/P = 5), higher stability (approximate to 40% higher binding affinity and up to 30% less morphological deformation), and are less prone to aggregation measured by nanoparticle tracking analysis over a period of one month. Furthermore, these physical attributes contribute up to 19% higher in cell viability at N/P = 5, while the gene silencing of enhanced green fluorescent protein remains constant in a human cell line. Control of particle properties is necessary to advance siRNA-based delivery; the CAD preparation represents a physical complement to chemical design modifications, which can be readily transferred among research labs and utilized for alternative polymer systems.