Garlic cultivation in tropical regions, such as the Brazilian Cerrado, faces the problem of secondary growth in the field induced by climatic conditions, which affects bulb quality and value. Clove essential oil (CEO) contains high levels of eugenol, which has the potential as an eco-friendly plant growth retardant (PGR) capable of reducing or inhibiting the secondary growth of bulbs in garlic cultivation. In this study, field experiments were carried out in two consecutive years (winter 2021 and 2022), spraying garlic plants with different concentrations of emulsion of CEO (0.0, 0.2, and 0.4%) in the differentiation phase; for comparison, the effects of water deficit, a prevalent agricultural technique in the region, were also evaluated. At a dose of 0.4%, the CEO reduced the prevalence of secondary growth and split bulbs without affecting yield. The mode of action of PGR was investigated by analyzing photosynthetic, enzymatic, and metabolomic parameters. The plants reduced amylolytic activity, and the photosynthetic parameters, after 7 days, were restored in both treatments. The analysis of the metabolomic profile of garlic leaves revealed changes in the pathways associated with the biosynthesis of fatty acids, wax, cutin, and suberin in plants treated with CEO, indicating possible damage to the surface coating of the leaf.