We followed the process of enzymatic digestion of ganglioside GD1a, operated by sialidase on aggregated micelles. The product is the ganglioside GM1, lacking the external sialic acid. The structural aspects and the kinetics connected to the process occurring on a fragmented-condensed substrate, the ganglioside micelles, are investigated by small angle X-ray scattering (SAXS). Observed at short times, the kinetics of the reaction shows a transient step-like decay, while it tends to a smooth Michaelis-Menten kinetics in the late stages. We propose a model, based on the fragmented-condensed nature of the substrate, that well reproduces the experimental observation without invoking any feedback mechanism in the reaction, usually required for an oscillatory behavior. The model predicts an initial regime dominated by the strict enzyme substrate interaction, with a step-like appearance.