Thymus carnosus Boiss. is a near-threatened species, and, as for many species, its potential for medicinal purposes may be lost if measures towards plant protection are not taken. A way of preserving these species is to increase knowledge about their medicinal properties and economic potential. Thus, with the objective of studying the potentiality of introducing T. carnosus as a crop, the stability of the phytochemical profile of T. carnosus was studied during a period of three years by comparing the phytochemical profile of extracts obtained from plants harvested in two different edaphoclimatic locations, as well as by comparing the respective bioactivities, namely, antioxidant, antidiabetic, antiaging, and neuroprotective activities. It was reported, for the first time, the effect of annual variation and geographic location in the phytochemical composition of aqueous decoction and hydroethanolic extracts of T. carnosus. In addition, the presence of two salvianolic acid B/E isomers in T. carnosus extracts is here described for the first time. Despite the variations in phytochemical composition, according to harvesting location or year, T. carnosus extracts maintain high antioxidant activity, assessed by their capacity to scavenge ABTS•+, •OH , NO•, O2•− radicals, as well as to prevent β-carotene bleaching. All extracts presented significant potential to inhibit acetylcholinesterase (AChE), tyrosinase, and α-glucosidase, denoting neuroprotective, anti-aging, and anti-diabetic potential. In conclusion, the vegetative stage and location of harvest are key factors to obtain the maximum potential of this species, namely, a phytochemical profile with health benefit bioactivities.