Pedotransfer function (PTF) approach is a convenient way for estimating difficult-to-measure soil properties from basic soil data. Typically, PTFs are developed using a large number of samples collected from small (regional) areas for training and testing a predictive model. National soil legacy databases offer an opportunity to provide soil data for developing PTFs although legacy data are sparsely distributed covering large areas. Here, we examined the Indian soil legacy (ISL) database to select a comprehensive training dataset for estimating cation exchange capacity (CEC) as a test case in the PTF approach. Geostatistical and correlation analyses showed that legacy data entail diverse spatial and correlation structure needed in building robust PTFs. Through non-linear correlation measures and intelligent predictive algorithms, we developed a methodology to extract an efficient training dataset from the ISL data for estimating CEC with high prediction accuracy. The selected training data had comparable spatial variation and nonlinearity in parameters for training and test datasets. Thus, we identified specific indicators for constructing robust PTFs from legacy data. Our results open a new avenue to use large volume of existing soil legacy data for developing region-specific PTFs without the need for collecting new soil data.