The development of smart materials capable of separating dihydrogen isotopologues has risen recently. Among potential candidates, the flexible MIL-53 (Al) has been gaining attention due to its structural flexibility providing the so-called ‘’breathing mechanism’’ that can be useful to separate hydrogen isotopologues selectively. In the present work, an in situ continuous wave electron paramagnetic resonance investigation has been proven as a sensitive technique to follow the isotopologue-selective adsorption-desorption of dihydrogen species on the paramagnetic metal-doped MIL-53 (Al_0.99Cr_0.01) and MIL-53 (Al_0.99V_0.01), respectively. The presence of paramagnetic spin probes such as Cr³⁺ and V⁴⁺ inside the MIL-53 framework allows for monitoring the framework transition including the 2^nd transition step that selectively occurs at p>100 mbar when D₂ gas is adsorbed on the pores at 23 K. Furthermore, investigation of D₂ desorption from MIL-53 (Al_0.99V_0.01) by temperature-dependent hyperfine spectroscopy provides a more detailed analysis of the D₂ desorption process on a microscopic scale with respect to the embedded spin probe.