Berberis integerrima L. belongs to the Berberidaceae family and is one of the small fruits with many medicinal properties, which is considered among the horticultural products with high plant diversity and favorable genetic reserves. This research aimed to study barberry's phenological, morpho-physiological, and biochemical attributes in five different habitats in Kerman province, Iran (Bam, Jiroft, Anbarabad, Raber, and Baft) during 2019-2020. The results of the phenological traits showed that the Jiroft and Anbarabad habitats have the maximum number of days until the end of vegetative growth, the number of days from activation of buds to the beginning of fruit formation, the number of days until the physiological maturity of the fruit, the number of days from activation of buds to fruit coloring, and the lowest number of days until flowering. The mean comparison showed that in terms of yield, the investigated habitats from the highest production to the lowest included Anbarabad> Baft> Bam> Rabar> Jiroft. The highest average traits of panicle length (43.38 cm), number of fruits per panicle (26.6), 1000-fruit weight (141.9 g), 1000-seedless fruit weight (128.4 g), seed length (1.16 mm), seed diameter (0.97 mm), fruit length and diameter (19.03 and 5.41 mm), yield (16.69 kg per stem), and the number of thorns 10 cm (13.5 pieces) was observed in Anbarabad habitat. The yield was negatively and significantly correlated with fruit length, titratable acidity, anthocyanin, DPPH, and phenol. Interestingly, soil nitrogen, phosphorus, and potassium had a positive effect on increasing the barberry yield. On the other hand, increasing the longitude, latitude, and altitude decreases yield. Anbarabad and Jiroft habitats had the highest and lowest averages of pH, titratable acidity, total soluble solids, chlorophyll, and carotenoid content, respectively. Generally, the results of this study indicate a high genetic diversity in phenological, morphological, chemical, and physiological aspects in different habitats. Moreover, the results showed that Anbarabad was significantly superior in phenological, morphological, yield, and phytochemical traits compared to other ecotypes.