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The formation of colloidal AlPO-5 nanocrystals were studied under hydrothermal and microwave conditions in the presence of a new templating agent, 1-ethyl-2,3-dimethylimidazolium hydroxide ([edmim]OH). The syntheses were performed by varying the synthesis conditions, i.e. crystallization time, heating temperature, molar composition and synthesis method. The study revealed that the synthesis parameters had profound effects on crystal growth and physico-chemical properties of AlPO-5 nanocrystals. The resulting AlPO-5 nanocrystals were colloidally stable and the crystallite size with defined shapes can be controlled in the range of 50–900 nm. Moreover, this study demonstrated a facile and fast microwave synthesis method whereby AlPO-5 nanocrystals could be obtained within several minutes instead of hours. The microwave-synthesized AlPO-5 nanocrystals had higher water sorption capacity, higher energy density and fast water desorption than the hydrothermal-synthesized counterpart making it a promising material for water sorption applications.