In the manufacturing of advanced therapy medicinal products (ATMP) the need of technologies transfer from traditional lab bench work to therapies’ production and commercialization phases became a bigger challenge. Due to the process requirements of ATMP manipulation, a high sterility assurance is required all the way through the workflow process; from the sample collection to the cell handling and gene editing up to final fill and finish formulation. Isolators technology become a natural next step to increase cell and gene therapies production and their quality control. Recently developed isolators allow for upstream, downstream and aseptic filling steps to be performed in a closed system with a validated aseptic control environment avoiding cross-contamination. In our first case study, we show the production of CAR T-cell medicinal product by using an integrated multi-chamber and flexible isolator system, developed to follow and support each step from the T-cell activation up to the gene editing and final cell suspension preparation. The second case study focus the production of mesenchymal stem cell-based product in a compact modular isolator system with fast material transfer options. Furthermore, in order to explore alternative ways to decontaminate sensitive material, i.e. living cells, we performed research studies focused on the bioburden reduction. In addition, our validated H2O2 decontamination cycles have been tested for penetration studies through various cell containers. Our preliminary data suggest that a necessary bioburden reduction can be achieved by using H2O2 containing solutions to decontaminate materials prior entry into the isolators. Various containers and primary packaging materials were tested. Our data showed that ready to use closed vials were the most resistant to the sterilant ingress, but other transfer solutions are available for permeable and vented containers. In conclusion, rapid transfers of cells and other sensitive materials can be achieved in a safe manner to protect product quality.