Opuntia ficus‐indica fruits have an important nutritional value and show several biological properties. This work studied the fruit physicochemical characteristics of two wild ecotypes (“Green” and “Orange”) and two cultivars (“Rossa” and “Gialla”) from Portugal. The results showed that the largest and heaviest fruits were those from ecotype “Orange,”, whereas the wild ecotype “Green” had fruits with firmer flesh. The fruit peels of cultivars “Rossa” and “Gialla” presented the highest fibre content. Glucose was the major carbohydrate in the fruits, particularly in the peels. Malic acid was the sole organic acid in both peels and pulps of all samples. The betacyanins’ content was higher in fruits of the “Rossa” cultivar, and the higher betaxanthins’ content was present in the peel of the cultivar “Gialla.” Peels of all samples generally had higher amounts of betalains than the pulps. The peel was a better scavenger of DPPH and ABTS free radicals than the pulp. Practical application The wastes of diverse food industries have revealed the presence of bioactive compounds with added value. The fruits of Opuntia ficus‐indica are appreciated for possessing biological attributes, nevertheless the peel generally is not used. The present work shows that the pigments (betalains) are predominantly found in the peel. Moreover, the in vitro antioxidant activity was also higher in this part of the fruit, independent on the ecotype or cultivar studied. Such results might trigger the interest for these residues from which pigments and bioactive compounds can be extracted, and, as extracts, can be used in diverse domains particularly in food and pharmaceutical industries.