The Internet of Things (IoT) paradigm is gradually finding its way in virtually every industry; however, beyond adding more sensors and measuring and controlling previously inaccessible domains, it is also about transforming ‘legacy’ approaches to control systems, such as those used in Building Management Systems (BMS), by leveraging on the advantages brought by Cyber Physical Systems (CPS). The purpose of this paper is to address several issues gradually emerging in the process of applying the CPS and IoT paradigms to revolutionise BMS. The results of this on-going research aim to help avoid potential pitfalls and provide a sound platform for taking advantage of the benefits brought by this technology in a feasible, effective and controlled manner. More specifically, the paper will address i) the changing meaning of interoperability in the context of the explosion in the number of IoT devices, ii) the need for guidance in adopting sustainable CPS and IoT platforms supporting BMS, based on appropriate non-functional and viable systems principles, iii) emerging issues in the BMS ‘cloudification’ endeavour and iv) the lack of data sources’ correlation resulting in sub-optimal data quality and detail in using Big Data technologies to enable effective analytics for prompt BMS decision-making.