In nutrient-poor ecosystems, certain plant families have evolved specific adaptations for phosphate acquisition, namely cluster roots or proteoid roots. Cluster rooted species have a unique suite of adaptations that enable them to survive in nutrient poor ecosystems, such as the Fynbos biome of South Africa. The Fynbos biome has heterogeneous soils which caused radiation of varying soil pH within small localised areas. Previous studies on cluster rooted species ignored the possibility that cluster root functioning may differ at varying soil pH levels and soil types. Therefore, two native Fynbos protea species, Protea cynaroides (L.) L. and Protea obtusifolia H.Buek ex Meisn. were compared to assess the impact of different soil pH levels on organic acid metabolism and exudation in cluster rooted species. Our results show that cluster roots of the acidic-soil grown P. cynaroides is more effective and more efficient than that of the alkaline-soil grown P. obtusifolia. Our findings indicated that the mechanisms for P acquisition vary greatly, depending on substrate and plant organ type. This suggested that the metabolism of each species is adapted to specific soil pH and that these species have evolutionary adapted their P acquisition mechanisms for these extreme soils. The limited nutrient availability and variation in soil pH South African soils has led to various localised adaptations for cluster rooted species.