Solar ultraviolet (UV) radiation mainly includes UVA (320–400 nm). UVA intensity varies depending on the season and geographic location, while it is projected to rise owing to climate change. Since it elicits secondary metabolism, additional knowledge on the UVA dependence of phytochemical production is required for both farmers and processors, particularly under natural settings. In this field study, the pheno-morphological traits and essential oil composition responses to UVA intensity were addressed in three Thymus species [T. daenensis (endemic to Iran), T. fedtschenkoi (semi-endemic), T. vulgaris (common thyme)]. During growth, three UVA levels (ambient, enriched, excluded) were realized in combination with spraying protectants [water (control), melatonin, glutathione, iron-zinc nanofertilizer]. In T. daenensis, enriched UVA caused early flowering. The height of T. daenensis was the longest under enriched UVA, and the shortest under excluded UVA. In control plants, enriched and excluded UVA stimulated the accumulation of oxygenated metabolites in T. daenensis and T. fedtschenkoi. Altogether, under enriched UVA some phenolic compounds (e.g., thymol, carvacrol, γ-terpinene) increased in the essential oil of all three species, but others decreased. In all taxa, glutathione caused a significant essential oil content reduction. Iron-zinc nanofertilizer increased essential oil accumulation in T. daenensis and T. vulgaris. Treatments also induced an alteration of the essential oil composition. In conclusion, cultivation regime effects on the essential oil quality (composition) and quantity were strongly species dependent. T. deanensis underwent the most consistent enhancement under UVA, making the species more adaptable to climate change, whereas T. fedtschenkoi the least.