The discovery of new inorganic building units for metal–organic framework (MOF) synthesis remains challenging. We hypothesized that incorporation of X-type halogen capping ligands on indium-building units would yield a series of previously unknown frameworks and the placement of the halogen could lead to framework isomerism. Herein we report the synthesis of three new MOFs; two (YCM-31 and YCM-32) contain an [In(CO2R)3Cl]− secondary building unit (SBU) and are framework isomers of each other. A third new MOF, ZJU-28′, contains an [In(CO2R)4]− SBU and is a framework isomer of the known MOF ZJU-28. The conditions to control the syntheses of these isomers through ammonium-cation templation, along with the rationale for their formation are discussed.