This study aimed to compare the chemical composition of aqueous extracts from different aerial plant parts (leaves, stems, and flowers) of Onopordum nervosum ssp. platylepis growing in different regions (Sousse, Kairouan, and Nabeul) in Tunisia, as well as their antioxidant and milk-clotting properties for both spontaneously grown and cultivated plants. Results showed that phenolic composition varies significantly among ecotypes and plant organs (p < 0.05), with flowers containing the highest amounts of total phenols and flavonoids in both plant types. The flowers from Nabeul (NA) region showed the highest amounts of total phenols and higher phenolic contents compared to leaves and stems, with 44.75 mg GAE/g and 39.79 mg GAE/g in spontaneous and cultivated plants, respectively. However, flowers of spontaneously plants grown in Sousse (SO) showed the highest total flavonoid contents (11.42 mg QE/g). Additionally, the findings indicated that flowers contained higher concentrations of mono- and disaccharides than leaves and stems. The antioxidant activity showed that the radical scavenging activity of O. platylepis aqueous extracts is significantly affected by the organ and genotype (p < 0.05). NA genotype revealed the highest potency in inhibiting free radicals, with flowers having the lowest IC50s values in 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) tests, registering 0.13 ± 0.02 and 0.14 ± 0.01 mg/mL, respectively. Milk-clotting activity was limited to flowers of this thistle. Moreover, SO and NA genotypes were identified as the most potent populations to coagulate milk in spontaneous and cultivated plants. The principal component analysis confirms the organ and genotype variability in this thistle, with the first two axes explaining 64.15% of the variance and highlighting a distinct flower group. The obtained results suggest that the domestication of this thistle could be useful for the conservation of biodiversity and the promotion of genotypes with potential technological properties.