<p>Droplet based microfluidics and automation are important technology to support bio-process and screening during the last years. Main objective of this review is to describe the current technology in monitoring secreting microbes at scale down level. During this study, questions and challenges are shown with relation to this approach specifically in droplet based microfluidics as well as in miniaturized platforms focused on screening of certain metabolites. Relevant challenges to both technologies are described in this article from a technical overview, those that are associated with the control of secondary metabolites as well as growth parameters during microbe cultivation with focus on <i>Y. lipolidica, S. lividians</i> and <i>C. glutamicum</i>. In order to achieve the objective, six studies highlighted in production of metabolites as polyphenols are discussed by using a narrative review as well as the relevancy of analytical methods that are associated with verify development of heterologous microorganisms during bioprocess.</p> Graphical Abstract <p></p>