PDMS microfluidic systems have been instrumental in better understanding couplings between physical mechanisms and bacterial biofilm processes, such as hydrodynamic effects. However, precise control of the growth conditions, for example the initial distribution of cells on the substrate or the boundary conditions in a flow system, has remained challenging. Furthermore, undesired bacterial colonization in crucial part of the systems, in particular in mixing zones or tubing, are an important factor that strongly limits the duration of the experiments and therefore impedes our ability to study the biophysics of biofilm evolving over long periods of time, as found in the environment, in engineering or in medicine. Here, we develop a new approach that uses ultraviolet-C (UV-C) light emitting diodes (LEDs) to confine bacterial development to specific zones of interest in the flow channels. The LEDs are integrated into a 3D printed light guide that is positioned upon the chip and used to irradiate germicidal UV-C directly through the PDMS. We first demonstrate that this system is successful in controlling undesired growth of Pseudomonas aeruginosa biofilm in inlet and outlet mixing zones during 48 hours. We further illustrate how this can be used to define the initial distribution of bacteria, to perturb already formed biofilms during an experiment and to control colonization for seven days-and possibly longer periods of timetherefore opening the way towards long-term biofilm experiments in microfluidic devices. Our approach is easily generalizable to existing devices at low cost and may thus become a standard in biofilm experiments in PDMS microfluidics.