Emerging photovoltaics hold great promise to add to the existing solar cell market by either becoming cost competitive or accessing new, niche markets unavailable to current technologies. Unfortunately, wide adoption of these systems, in particular organic photovoltaics (OPVs) and perovskite photovoltaics, is hampered by overall poor performance in either efficiency (in OPVs) or in long-term stability (in perovskite photovoltaics). Designing better materials and optimizing device morphology/architectures, with the latter changing intrinsic material interfaces within the devices, has made progress to overcome some of these issues. Since these interfaces affect overall efficiency and stability, understanding interface chemistry (composition) and morphology is important in understanding overall device performance. Characterization of these interfaces requires techniques capable of probing the chemistry-morphology relationship at the nanoscale. Here, we use Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) and Atomic Force Microscopy (AFM) to characterize these material systems and their device interfaces. In P3HT:PCBM, a classic OPV system, we directly imaged the active layer buried morphology and determined the mixing length of the D/A interface, which is crucial for device performance and had yet to be measured. We determined, contrary to the general understanding, that thermal annealing in this system actually leaves the bulk heterojunction film mostly mixed. Our methodology provides a route to determining this D/A interface length for other OPV systems providing a new metric and insight for better device design principles. For MAPbI₃ perovskites, we studied interfacial behavior to understand light-induced degradation in functioning devices and electrical-induced degradation in films based on contact selection as well as visualized bias-induced ion migration. We determined that the PDI-EH electron transport layer hinders degradation; whereas, a PCBM electron transport layer allows and facilitates it. For electrical degradation, we determined that an ITO electrode induces more degradation than a platinum contact by measuring interface MAPbI₃/ITO mixing. And, by using lateral MAPbI₃ devices, we visualized ion migration due to an applied electric field. For perovskite devices, interfacial behavior dictates long-term performance. Overall, using a combination of ToF-SIMS and AFM to interrogate interfacial chemistry and morphology, we are working towards better devices through understanding limits on efficiency and stability.