This work deals with the use of a water/tert-butyl alcohol (TBA) system in the manufacturing process of poly-ε-caprolactone (PCL) nanoparticles, namely in the synthesis stage, using the solvent displacement method in a confined impinging jet mixer (CIJM), and in the following freeze-drying stage. The experimental investigation evidenced that the nanoparticles size is significantly reduced with respect to the case where acetone is the solvent. Besides, the solvent evaporation step is not required before freeze-drying as TBA is fully compatible with the freeze-drying process. The effect of initial polymer concentration, flow rate, water to TBA flow rate ratio, and quench volumetric ratio on the mean nanoparticles size was investigated, and a simple equation was proposed to relate the mean nanoparticles size to these operating parameters. Then, freeze-drying of the nanoparticles suspensions was studied. Lyoprotectants (sucrose and mannitol) and steric stabilizers (Cremophor EL and Poloxamer 388) have to be used to avoid nanoparticles aggregation, thus preserving particle size distribution and mean nanoparticles size. Their effect, as well as that of the heating shelf temperature, has been investigated by means of statistical techniques, with the goal to identify which of these factors, or combination of factors, plays the key role in the nanoparticles size preservation at the end of the freeze-drying process. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci