The interfacial behavior of quantum materials leads to emergent phenomena such as two dimensional electron gases, quantum phase transitions, and metastable functional phases. Probes for in situ and real time surface sensitive characterization are critical for active monitoring and control of epitaxial synthesis, and hence the atomic-scale engineering of heterostructures and superlattices. Termination switching, especially as an interfacial process in ternary complex oxides, has been studied using a variety of probes, often ex situ; however, direct observation of this phenomena is lacking. To address this need, we establish in situ and real time reflection high energy electron diffraction and Auger electron spectroscopy for pulsed laser deposition, which provide structural and compositional information of the surface during film deposition. Using this unique capability, we show, for the first time, the direct observation and control of surface termination in complex oxide heterostructures of SrTiO3 and SrRuO3. Density-functional-theory calculations capture the energetics and stability of the observed structures and elucidate their electronic behavior. This demonstration opens up a novel approach to monitor and control the composition of materials at the atomic scale to enable next-generation heterostructures for control over emergent phenomena, as well as electronics, photonics, and energy applications.