The present paper discloses a new alternative method for the isomerization of eugenol to isoeugenol where mesoporous materials containing niobium are used as solid base catalysts, affording good yields of isomerized product and being environmentally friendly. Nb-containing MCM-41 mesoporous materials were modified with alkaline cations (Li, Na, K, Rb and Cs) and characterized by BET, FTIR, XRD, and UV-vis techniques. The prepared materials were tested in the isomerization of eugenol to isoeugenol by sonochemical and thermally-activated reactions. Li, Na, K, Rb, and Cs/NbMCM-41 catalysts are active catalyst for the preparation of isoeugenol, and selective to the trans-isomer. Rb/NbMCM-41 sample is the optimum catalysts for the reaction. This result is in accordance with the calculated basicity observed during the Knoevenagel probe reaction of basicity. Conversions around 90% are obtained when using Rb-NbMCM-41 catalysts, with 90% selectivity to trans-isoeugenol, under ultrasound activation. In contrast, conversion around 72% with 90% selectivity is attained under classical thermal activation. The catalysts were reused four times without a substantial decrease of activity.