Marine bacteria are increasingly explored as alternative microbial platforms for the production of high-value biopharmaceuticals, owing to their distinctive physiological and biochemical features. In this study, we focus on the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), an unconventional host that has proven capable of producing soluble and active human Cyclin-Dependent Kinase-Like 5 (hCDKL5). This serine/threonine kinase is essential for neuronal development as its deficiency causes CDKL5 Deficiency Disorder, a severe and currently untreatable neurodevelopmental disease. Recombinant production of hCDKL5 represents a necessary prerequisite for the development of enzyme replacement therapy as a potential therapeutic strategy; however, the current production process remains insufficient for industrial translation. To address this limitation, we developed and implemented dedicated analytical methods to assess both the quantity and functional quality of recombinant hCDKL5. Production yields were evaluated using a customised quantitative sandwich Enzyme-Linked Immunosorbent Assay (ELISA) specifically detecting full-length hCDKL5, while protein functionality was assessed by mass spectrometry-based quantification of autophosphorylation levels, a key indicator of kinase activity. These tools were applied to characterise hCDKL5 expression under different growth conditions. Overall, this work establishes an integrated analytical framework aligned with a Quality by Design approach, providing a robust basis for future process optimisation toward scalable hCDKL5 production.