We compare the microfluidic manufacturing of polycaprolactone-block-poly(ethylene oxide) (PCL-b-PEO) nanoparticles (NPs) in a single-phase staggered herringbone (SHB) mixer and in a two-phase gas-liquid segmented mixer. NPs generated from two different copolymer compositions in both reactors and at three different flow rates, along with NPs generated using a conventional bulk method, are compared with respect to morphologies, dimensions, and internal crystallinities. Our work, the first direct comparison between alternate microfluidic NP synthesis methods, shows three key findings: (i) NP morphologies and dimensions produced in the bulk are different from those produced in a microfluidic mixer, whereas NP crystallinities produced in the bulk and in the SHB mixer are similar; (ii) NP morphologies, dimensions, and crystallinities produced in the single-phase SHB and two-phase mixers at the lowest flow rate are similar; and (iii) NP morphologies, dimensions, and crystallinities change with flow rate in the two-phase mixer but not in the single-phase SHB mixer. These findings provide new insights into the relative roles of mixing and shear in the formation and flow-directed processing of polymeric NPs in microfluidics, informing future reactor designs for manufacturing NPs of low polydispersity and controlled multiscale structure and function.