Microwave assisted isomerization of estragole to anethole was studied over MgAl and NiAl layered double hydroxides with different M(II)/Al atomic ratios as solid base catalysts. Reactions under microwave overcame the challenges like higher reaction temperature, longer time, larger solvent volume and unproductive recyclability that were encountered with conventional thermal heating for this reaction. MgAl4 (catalyst with Mg/Al atomic ratio of 4.0) gave maximum conversion of 99% with a substrate to catalyst weight ratio 2:1 at 140 °C in 90 min using 4 ml DMF. A good correlation was obtained between the activity and Brønsted basicity derived using Hammett studies. Solvent with high polarity and high boiling point assisted the reaction and the catalyst was reusable for up to six cycles without significant loss in activity. Studies extended for different alkenyl aromatics under optimized conditions over MgAl4 revealed a very high conversion (>97%) for estragole and allylbenzene (>99%) while poor conversion for eugenol (19%). The variation in isomerization activity of alkenyl aromatics was rationalized with DFT calculations. The B3LYP/6-31+G* calculated results revealed that the conversion of these alkenyl aromatics was dependent on the substituents attached to the aromatic ring and governed by the pKa of the reactive sites in such systems. Methodology reported here offers an alternate energy efficient and environmentally benign route for the synthesis of alkenyl aromatics, which are extensively used as perfumery chemicals.