The emergence of new bioprocessing technologies for integrated, continuous biotherapeutics manufacturing has instigated a need to establish new process analytical technologies (PAT) that are able to monitor product attributes that ultimately define the safety and efficacy of the drug. The aim of this Engineering Doctorate has been to develop new analytical technologies that address a problematic facet of biologics manufacturing: the propensity for proteins to unfold and aggregate. A high-throughput system for circular dichroism (CD) and fluorescence spectroscopy has been developed for automated capillary-based structural analysis of biotherapeutics loaded in 96-well plate format. The system was used to examine the conformational stability of monoclonal antibody (mAb) using chemical denaturation (urea) and low pH elution buffers. Subsequently, an in-line methodology was developed for monitoring structural changes of mAb immediately following affinity chromatography (Protein A/Protein G/Byzen Pro) through measured changes in CD\(_{240 nm}\) g-factor and fluorescence \(\lambda_{max}\), establishing a new technique for real time release testing in bioprocessing. Finally, a fused silica microcapillary (220 μm i.d.) flow cell was developed for high-throughput/in-line CD analysis of concentrated protein solutions and further demonstrated as being suitable for the alignment of macromolecules for rapid linear dichroism (LD) detection.