Nitride materials are critical for a range of applications, including UV-visible light emitting diodes (LEDs). Advancing the performance, reliability and synthesis of AlGaN/GaN and InGaN/GaN heterojunction devices requires a systematic methodology enabling characterization of key metric like alloy composition, thickness and quality possibly in real time. This contribution reports on the real time characterization of the plasma assisted molecular beam epitaxy of AlGaN/GaN and InGaN/GaN heterostructures. Spectroscopic ellipsometry real time monitoring has revealed a number of key process and material iusses, such as the roughening of the GaN templates depending on plasma exposure during the substrate cleaning step, the composition of the alloy and the growth mode. Parameters like the plasma conditions, the surface temperature and the atomic flow ratio are investigated to understand the interplay process-material composition-structure-optical properties.