Amorphous aluminophosphates are industrial catalysts that are active in aldol-type condensations, dehydration and alkylation. The intrinsic nature of the active sites present in these materials is poorly understood. Herein we report a comparative investigation of the catalytic active sites in amorphous and crystalline aluminophosphates (AFI topology) and their corresponding iron-containing analogues, employing Claisen-Schmidt condensation of acetophenone and benzaldehyde as the test reaction. Secondary porosity generated via the soft-templating approach in hierarchically-porous HP FeAlPO-5, and the presence of large mesopores in amorphous Am FeAlPO resulted in improved mass-transport and high conversion of carbonyls. The nature and concentration of the active acidic sites within these materials were characterized by pyridine-DRIFTS and propylamine-TPD studies and was shown to play a crucial role in the activation of carbonyl groups and better catalytic performance. Am FeAlPO(5) nearly outperformed HP FeAlPO-5, thus providing a promising alternative for expanding scope in industrial and pharmaceutical applications.