Following ionization by an extreme ultraviolet (XUV) attosecond pulse train, a polyatomic molecule can be promoted to more-than-one excited states of the residual ion. The ensuing relaxation dynamics is often facilitated by several reaction coordinates, making them difficult to disentangle by usual spectroscopic means. Here, we show that in atto-chemistry isotope labelling can be an efficient tool for unraveling the relaxation pathways in highly excited photo-ionized molecules. Employing a XUV pump pulse and a near-infrared probe pulse, we found the nuclear as well as coupled electron-nuclear dynamics in ethylene to be almost 40% faster compared to its deuterated counterpart. The findings, which are supported by advanced non-adiabatic dynamics calculations, led to the identification of the relevant nuclear coordinates controlling the relaxation. Our experiment highlights the relevance of ultrashort XUV pulses to capture the isotopic effect in few-femtosecond molecular photo-dynamics.