The lack of process analytical technologies able to provide real‐time information and process control over a biopharmaceutical process has long impaired the transition to continuous biomanufacturing. For the monoclonal antibody (mAb) production, aggregate formation is a major critical quality attribute (CQA) with several known process parameters (i.e., protein concentration and agitation) influencing this phenomenon. The development of a real‐time tool to monitor aggregate formation is then crucial to gain control and achieve a continuous processing. Due to an inherent short operation time, miniaturized biosensors placed after each step can be a powerful solution. In this work, the development of a fluorescent dye‐based microfluidic sensor for fast at‐line PAT is described, using fluorescent dyes to examine possible mAb size differences. A zigzag microchannel, which provides 90% of mixing efficiency under 30 s, coupled to an UV–Vis detector, and using four FDs, was studied and validated. With different generated mAb aggregation samples, the FDs Bis‐ANS and CCVJ were able to robustly detect from, at least, 2.5% to 10% of aggregation. The proposed FD‐based micromixer is then ultimately implemented and validated in a lab‐scale purification system, demonstrating the potential of a miniaturized biosensor to speed up CQAs measurement in a continuous process.