Quantifying the impact of environmental physicochemical changes on the microstructure of lipid delivery systems is challenging. Therefore, we have developed a methodology to quantify the coalescence of oil-in-water emulsion droplets during lipid digestion in situ on a single droplet level. This technique involves a custom-made glass microfluidic platform, in which oil droplets can be trapped as single droplets, or several droplets per trap. The physicochemical environment can be controlled, and droplet digestion, as well as coalescence, can be visualized. We show that the exchange of the physicochemical conditions in the entire reaction chamber can be reached in under 30 s. Microparticle image velocimetry allowed mapping of the flow profile and demonstrated the tuneability of the shear profile in the device. The extraction of quantitative information regarding the physical characteristics of the droplets during digestion was performed using an automated image analysis throughout the digestion process. Therefore, we were able to show that oil-in-water emulsions stabilized by proteins coalesced under human gastric conditions. This coalescence delayed the overall lipid digestion kinetics. The droplets that coalesced during digestion were hydrolyzed 1.4 times slower than individually trapped droplets. Thus, the microstructural evolution of lipid delivery systems is a crucial factor in lipid digestion kinetics. This novel technique allows the simultaneous quantification of the impact that the physicochemical environment has on both the lipid droplet microstructure and the lipid release patterns.