Here we present a highly customisable image-based fuzzy logic control (FLC) method for pressure-driven droplet microfluidics. The system is designed to position droplets of different sizes in microfluidic chips of varying channel size in the centre of the region of interest (ROI) using two parallel multiple input single output (MISO) FLCs. Overall, 95.1% of the droplets with an average displacement of 2.5 μm could be kept within the ROI during the pre-defined time intervals of up to 10 s. This is achieved by pre-determined pressure values that are kept constant during this time. The control principle was tested on different pressure controllers and microfluidic chips varying in material, channel layout and cross section. Droplet volumes ranged from a few hundred picolitres to a tenth of a microlitre. The droplets were composed of deionised water or contained two concentrations of S. cerevisiae. The average processing time was 12.5 seconds. This makes the method suitable for studying several hundred pre-sorted droplets from high-throughput screening (HTS) experiments.