X-ray photoemission spectroscopy (XPS) depth profiling using monatomic Ar+ ion etching sources is a common technique that allows for the probing of the vertical compositional profiles of a wide range of materials. In polymer-based organic photovoltaic devices, it is commonly used to study compositional variations across the interfaces of the organic active layer with charge extraction layers or electrodes as well as the vertical phase separation within the bulk-heterojunction active layer. It is generally considered that the damage induced by the etching of organic layers is limited to the very top surface, such that the XPS signal (acquired from the top μ10 nm of the layer) remains largely unaffected, allowing for a reliable measurement of the sample composition throughout the depth profile. Herein, we investigate a range of conjugated polymers and quantify the depth of the damage induced by monatomic etching for Ar+ ion energies ranging from 0.5 to 4 keV using argon gas cluster ion beam depth profiling. The results demonstrate that even when etching with the lowest available monatomic ion energy for as little as 3 s, the damaged polymer material extends deeper into the bulk than the XPS probing depth. We show that the damaged material distorts the compositional information obtained by XPS, resulting in erroneous depth profiles. Furthermore, we propose that only gas cluster ion beam etching sources should be used for depth profiling of organic conjugated polymers, as those induce significantly less damage and maintain the compositional information throughout the entire profile.