DUT-49(Cu) is a well-studied representative of flexible mesoporous frameworks, in particular, famous for long-lived overloaded metastable states in the presence of a variety of gases at defined temperatures, leading to “negative gas adsorption” transitions. Important mechanistic insights into these transitions in DUT-49 were obtained via in situ powder X-ray diffraction (PXRD) studies conducted in parallel to gas physisorption. However, for strongly X-ray absorbing probe molecules, such as xenon, such studies are not feasible, even if synchrotron radiation is used. Here we employ in situ electron paramagnetic resonance spectroscopy (EPR), PXRD, and adsorption isotherm measurements to explore the phase transformations in DUT-49(Cu) in the presence of xenon and compare its properties with the corresponding adsorption/desorption behavior of ethylene for this material. The antiferromagnetically coupled CuII–CuII dimers in the paddle-wheel (PW) units of this pillared layer MOF serve as local magnetic probes in the in situ EPR measurement. These experiments allowed us to monitor the op ↔ cp phase transformations during the xenon physisorption through the structural changes at the PW units encoded in the zero-field splitting parameters of the S = 1 state of the CuII dimers. The EPR data indicates an expansion of the unit cell for the cp phase in the presence of xenon. This novel EPR-derived insight into the phase transformation phenomena of the xenon-loaded DUT-49(Cu) could be validated by combined in situ EPR, PRXD, and adsorption isotherm measurements for ethylene adsorption over the same MOF material in a comparable temperature range.