Polydopamine is a nature inspired functional material with promising applications in a plethora of fields due to its structural, chemical, and optical properties. While there is significant interest in the preparation of polydopamine based nanomaterials that take advantage of its properties, less attention has been given to the optimisation of the synthetic process, which typically involves the oxidative self-polymerisation of dopamine under basic pH and requires 24–72 h for reaction completion. The present work investigated the kinetics of polydopamine formation in the presence of Pluronic P-123 (PEG-PPG-PEG) micelles acting as a soft template, in low monomer concentrations (that promote particle growth instead of nucleation) as a function of temperature and pressure. Simultaneous increase of pressure and temperature (up to 50 °C and 5 bar O2) was found to significantly reduce the reaction time to 20–40 min without compromising the particle quality. Based on the results of the kinetic investigation, the polydopamine synthesis was translated into a continuous process utilising a millifluidic co-axial membrane reactor with a focus on ease of use, process conditions’ reproducibility and safety of operation. The reactor produced nanoparticles similar to the batch synthesis and resisted fouling (which is generally expected in a compact flow reactor) due to the action of the P-123 surfactant. Due to the nontoxic process that utilises only biocompatible materials and oxygen as the oxidising agent, and the melanin-like structure of polydopamine, photothermal heating of the synthesised nanoparticles under concentrated IR irradiation at 808 nm light was studied, as this can potentially be used for photo-induced hyperthermia. The hyperthermia threshold of 10 °C temperature increase at relatively low laser power settings (fluence 1.77 W/cm2) was achieved, making it a promising candidate for this application.