The salinity of soil is among the most important abiotic stresses which limit agricultural productivity worldwide. The effects of salinity on growth, nutrient partitioning, chlorophyll, leaf relative water content, osmolytes accumulation and antioxidant compounds of pepper (Capsicum annuum L.) cultivars ('Granada', 'Goliath' and 'Nobili'), widely used in Cameroon, were investigated. Plants were subjected to four levels of NaCl (0, 50, 100 and 200 mM) at early seedling growth stage of plant development. Application of NaCl treatment led to a significant increase in total soluble sugars, proline, soluble proteins, total free amino acids content, peroxydase and superoxide dismutase activity and total phenolic content in salt-tolerant 'Granada' and 'Nobili' compared to salt-sensitive 'Goliath' and untreated plants, on the contrary, decreased in root dry weight, shoot dry weight, number of leaves, shoot length, stem diameter, total leaf area, chlorophyll and leaf relative water content in 'Goliath' at low salinity level. Flavonoid content, K, Ca and Mg concentrations were significantly reduced with increasing salinity in all cultivars. The highest Na concentrations were detected in the leaves while the lowest were recorded in the roots of 'Goliath' at high salinity level. The salt sensitivity of 'Goliath' seems to be increased osmotic adjustment through the strongly accumulation of Na in leaves while the salt tolerance of 'Granada' was related to its induce of antioxidative enzyme system more efficiently, resulting in higher osmolytes accumulation under salinity. 'Granada' was more tolerant and stable in physiological and biochemical traits suggesting that it could be grown in salt-affected soils.