MPs (3-alkyl-2-methoxypyrazines) are grape-derived aroma compounds that are associated with detrimental herbaceous flavours in some wines. It is well known that several viticultural and environmental parameters can modulate MP concentrations in grapes, although comprehensive molecular studies have not been conducted in this field. Although the biosynthesis pathway of MPs has not been fully elucidated, four Vitis vinifera O-methyltransferase genes (VvOMT1-4) have been demonstrated to be involved in MP biosynthesis. We assessed whether sunlight restriction and abiotic stress induction have an impact on MP levels in grapes and wines from seeded and parthenocarpic fruits. Our results show that VvOMT1 and VvOMT3 expression correlates with 3-isobutyl-2-methoxypyrazine (IBMP) levels in seeded fruits during both abiotic stresses, whereas no correlation was found in parthenocarpic fruits. These results are discussed in the context of how different viticultural practices can modulate VvOMT gene expression, which has a direct impact on IBMP levels in wines.