Primula veris (cowslip) is an important medicinal–aromatic plant used traditionally for its expectorant and anti-inflammatory properties, as well as a valuable horticultural plant with ornamental value and agroalimentary interest (edible flowers and leaves). With extensive illegal harvesting across northern Greece to date, the long-term survival of Greek cowslip wild-growing populations seems compromised. With the aim to characterize the phytochemical content of locally adapted native genotypes of P. veris subsp. veris, we examined samples from 13 wild-growing populations sourced from 8 mountain areas along a longitudinal gradient of northern Greece. Flowers, leaves, and roots were separately evaluated with HPLC-PDA-MS for their chemical content to select the genotypes associated with the best phytochemical traits. The flowers were found to contain mainly flavonoids, isorhamnetin, quercetin, and kaempferol triglycosides, with varied population contents, generally higher in northwestern population samples with a colder and more humid climate; however, all in line with the European Medicines Agency’s (EMA) reports. The leaves were characterized by the prevalence of kaempferol and quercetin triglycosides, being generally higher than that of the flowers. In the roots, saponins were detected in relatively low percentages, and the phenolic glycosides were found up to nearly 2%. The results of this study suggest a potential specificity of the marginal Greek genotypes being at the edge of the species’ native distribution range in Europe and Asia. The phytochemical characterization herein supports the domestication process of Greek native cowslip genotypes. In turn, this may alleviate the overharvesting pressure in wild populations, thus contributing to species conservation and offering an incentive for farmers to sustainably cultivate at local scales well-adapted indigenous genotypes of high value.