The development and optimization of lipid nanoparticle (LNP) formulations through hydrodynamic mixing is critical for ensuring the efficient and cost-effective supply of vaccines. Continuous LNP formation through microfluidic mixing can overcome manufacturing bottlenecks and enable the production of nucleic acid vaccines and therapeutics. Predictive process models developed within a QbD Biopharma 4.0 approach can ensure the quality and consistency of the manufacturing process. This study highlights the importance of continuous LNP formation through microfluidic mixing in ensuring high-quality, in-specification production. Both empty and nucleic acid-loaded LNPs are characterized, followed by a TFF/buffer exchange to obtain process parameters for the envisioned continuous SPTFF. It is shown that LNP generation by pipetting leads to a less preferable product when compared to continuous mixing due to the heterogeneity and large particle size of the resulting LNPs (86−104 nm). Particle size by continuous formation (71 nm) and the achieved encapsulation efficiency (EE) of 88% is close to the targeted parameters for Pfizer’s mRNA vaccine (66−93 nm, 88). With the continuous encapsulation of nucleic acids in LNPs and the continuous production of mRNA in in vitro transcription, the basis for the holistic continuous production of mRNA is now established. We already showed that a fully autonomous process requires the incorporation of digital twins and a control strategy, with predictive process models and state-of-the-art PAT enabling real-time-release testing. This autonomous control can considerably improve productivity by about 15−20% and personnel as well as chemical reduction of about 30%. The results of this work complement this, laying the basis for fully continuous, bottleneck-free production of mRNA and other cell- and gene-therapeutic drug/vaccine candidates in a GMP- and QbD-compliant Biopharma 4.0 facilities on a flexible scale.