Microfluidic interlayer cooling has been demonstrated as a practical solution for the vertical stacking of high power microelectronics. Although a considerable amount of studies has been presented for single phase cooling with this approach, the flow boiling features in more complex arrangements have not been as thoroughly studied. The embedded cooling of microelectronics is feasible with the use of dielectric refrigerants, which are ideally used in two-phase conditions in order to exploit the latent heat of vaporization. In the present investigation, the two-phase cooling in silicon microgaps is assessed under variable power and heat transfer surface area densities. The dielectric refrigerant HFE-7200 is used as the working fluid under flow boiling conditions, analyzing useful characteristics such as the two-phase flow regime, heat transfer, and pressure drop. The present investigation uses a numerical model that is capable of predicting the relevant features of flow boiling phenomena through a mechanistic phase-change model. The results from this study demonstrate that multiple hotspots with variable pin densities can be effectively controlled, with relatively uniform temperatures, under flow boiling conditions with dielectric fluids.