Biosensors are self-sufficient devices utilizing biological elements (enzymes, antibodies, DNA, whole cells, tissues, etc.) in conjunction with a transducer (electrochemical, piezoelectric, optical, etc.) that coverts biological interactions into an electronic signal, which is a function of the concentration of the target analyte, allowing for both quantitative and qualitative measurements in real time. The wide variety of available biological systems and compatible transduction strategies make biosensing technology versatile, adaptable, and customizable to the needs of niche applications, such as environmental monitoring, production control or in vivo diagnostics. Whole (living) cells remain at the forefront of biosensor research as the most efficient biological elements (offering both, specific responses to a range of analytes and the insurmountable natural signal amplification schemes) that require easy handling, effortless assay procedures and simple set-ups to produce straightforward signals for risk assessments. In addition, whole cells biosensors have evolved to constitute a valuable tool in studying microbial ecology and gene expression in complex environments. Notwithstanding, designing such a system is not an easy task, necessitating inter-disciplinarity to handle operational (corrosivity, maintenance, disturbances in the growth pattern, surface tension and osmotic pressure effects, reduced water activity, changes in the cell morphology), metrological (activity, mass transfer limitations by diffusion, cell-to-cell communication, altered membrane permeability and media components availability) and economic parameters (to enhance the competitive advantage over conventional lab instrumentation). This paper presents a methodological framework for aiding whole cell biosensor design in terms of (i) efficient knowledge transfer for rapid problem solving, and (ii) expert system design/development for on-line fault detection.