The three-dimensional two-phase flow dynamics inside a microfluidic device of complex geometry is simulated using a parallel, hybrid front-tracking/level-set solver. The numerical framework employed circumvents numerous meshing issues normally associated with constructing complex geometries within typical computational fluid dynamics packages. The device considered in the present work is constructed via a module that defines solid objects by means of a static distance function. The construction combines primitive objects, such as a cylinder, a plane, and a torus, for instance, using simple geometrical operations. The numerical solutions predicted encompass dripping and jetting, and transitions in flow patterns are observed featuring the formation of drops, ‘pancakes’, plugs, and jets, over a wide range of flow rate ratios. We demonstrate the fact that vortex formation accompanies the development of certain flow patterns, and elucidate its role in their underlying mechanisms. Experimental visualisation with a high-speed imaging are also carried out. The numerical predictions are in excellent agreement with the experimental data.