In this work three disciplines – microfluidics, microbiology and microwave engineering – are utilized to develop a system for analyzing subpopulations of biofilms and their reaction to antibiotic treatment. We present handling strategies to destabilize a biofilm inside a microfluidic system down to aggregate sizes of<10 µm² as well as microfluidic structures for the flow-through filtration of the resulting cell suspensions. For the analysis of the cell populations by microwave electrical impedance spectroscopy, two novel calibration schemes are demonstrated to cover both, reflection as well as transmission measurements of dielectric fluids. The broadband calibration strategies are solely based on liquid standards and allow a precise long-term monitoring with a resolution up to Δε=6 ‰, while the error is kept below Δ=1.5 ‰ at 5 GHz. Combining these three research topics therefore will open up new ways for analyzing biofilm effects.