Incorporation of amino acid capping molecules (alanine (Ala), methionine (Met), phenylalanine (Phe), tryptophan (Trp), tyrosine (Tyr), and valine (Val)) in their zwitterionic form into archetypal [Zr6(μ3-O)4(μ3-OH)4]12+ clusters creates supramolecular frameworks in which the assembly of these highly charged discrete units with chloride counterions provides a unique combination of porosity, chirality, and proton conductivity. The supramolecular frameworks assembled from these cluster entities (i.e., ZrAla, ZrMet, ZrPhe, ZrTrp, ZrTyr, and ZrVal) are based on the counterbalancing of the cationic hexanuclear entities by chloride anions. The resulting structures provide porous structures (except ZrVal) with variability of chemical and structural stability based on their supramolecular interactions. Among these compounds, ZrPhe and ZrVal remain stable due to the presence of a double chelation-like interaction involving four hydrogen bonds formed between a chloride anion, two ammonium groups, and two coordinated water molecules from two adjacent hexanuclear units. The presence of multiple acidic proton positions and strong hydrogen-bond donor/acceptor groups on the water channels gives rise to easy proton conduction pathways within the structures. In fact, ZrPhe and ZrVal, together with ZrTyr, exhibit high proton conductivity values with varying dependencies on the atmospheric humidity. Finally, the correlation between proton conduction and porosity is discussed.