Nanoclay-enzyme complexes prepared form pure nanoclays isolated from ores or mines are the recent area of attention for their potential agriculture and biotechnological uses. The activity of nanoclay-enzyme complexes depends on both enzyme and nanoclay properties. However pure nanoclay seldom exists in natural soil conditions rather mixed with other soil clays specifically poorly ordered aluminosilicate. Thus, nanoclays isolated from three major soils (Vertisol, Alfisol, and Inceptisol) with or without poorly ordered aluminosilicates were used to comprehend phosphatase reaction occurring in the heterogeneous soil environment by preparing nanoclay-phosphatase complexes. Adsorption isotherms along with catalytic kinetics of organic phosphorus (P) hydrolysis by acid and alkaline phosphatases were studied. The adsorption of acid and alkaline phosphatases on nanoclay was rapid, thus its kinetics could not be ascertained. The adsorptions of acid and alkaline phosphatases were best described by the Freundlich equation (R2 = 0.82–0.99). Selected thermodynamic parameters i.e., changes in Gibbs free energy, entropy and enthalpy were calculated to interpret the energetics of the reactions. Results suggest that phosphatase adsorption to nanoclays was spontaneous, based on energetics. The process of acid and alkaline phosphatase adsorption were exothermic and enthalpy driven. The acid phosphatase is chemisorbed while alkaline phosphatase is physisorbed to the nanoclay surface. The presence of poorly ordered aluminosilicates in nanoclays increased the affinity of acid phosphatase for the substrate while the reverse was true for alkaline phosphatase. Immobilized acid phosphatase showed lower catalytic efficiency whereas alkaline phosphatase, when immobilized, resulted in significantly greater catalytic efficiency than the free enzyme. Therefore, the results of the present experiment emphasize the need to study soil nanoclay-enzyme complexes using nanocalys that coexist with other soil clays specifically poorly ordered aluminosilicates than pure nanoclays extracted from ores and mines. This knowledge could be used for regulating P availability and help alleviating P deficiency in the soils studied in the present investigation.