Stem cell-based therapeutic products could be the key to treat the deadliest current pathologies, ranging from neuro-degenerative to respiratory diseases. However, in order to bring these innovative therapeutics to a commercialization stage, reproducible manufacturing of high quality cell products is required. Although advances in cell culture techniques have led to more robust production processes and dramatically accelerated the development of early-phase clinical studies, challenges remain before regulatory approval, particularly to define and implement science-based quality standards (essential pre-requisites for national health agencies). In this regard, using new methodologies, such as Quality By Design (QBD), to build the production process around drug quality, could significantly reduce the chance of product rejection. This review-based work aims to perform a QBD approach to Mesenchymal Stem Cell (MSC) manufacturing in standard two-dimensional flasks, using published studies which have determined the impact of individual process parameters on defined Critical Quality Attributes (CQA). Along with this bibliographic analysis, parameter criticality was determined during the two main manufacturing stages (cell extraction and cell amplification) along with an overall classification in view of identifying the Critical Process Parameters (CPP). The analysis was performed in view of an improved standardization between research teams, and should contribute to reduce the gap towards compliant Good Manufacturing Practice (cGMP) manufacturing.