The binding of ammonium ions by two homooxacalix[3]arene-based receptors was studied using NMR spectroscopy and in silico methods. Both receptors are shown to endocomplex, even in a protic environment, a large variety of primary ammonium ions, including biomolecules. The binding mode is similar for all guests with the ammonium ion deeply inserted into the polyaromatic cavity and its NH3+ head nearly in the plane defined by the three oxygen atoms of the 18-crown-3 moiety, thus enabling it to establish three H-bonds with the ethereal macrocycle. The remarkable electronic, size, and shape complementarity between primary ammonium ions and the two cavity-based receptors leads to an unprecedented specificity for primary ammonium ions over secondary, tertiary, and quaternary ones. These binding properties were exploited for the selective liquid-liquid extraction of primary ammonium salts from water and for the selective recognition of lysine-containing peptides, opening new perspectives in the field of peptide sensing.