A well-established strategy to synthesize heterogeneous, metal-organic framework (MOF) catalysts that exhibit nanoconfinement effects, and specific pores with highly-localized catalytic sites, is to use organic linkers containing organocatalytic centers. Here, we report that by combining this linker approach with reticular chemistry, and exploiting three-dimensioanl (3D) MOF-structural data from the Cambridge Structural Database, we have designed four heterogeneous MOF-based catalysts for standard organic transformations. These programmable MOFs are isoreticular versions of pcu IRMOF-16, fcu UiO-68 and pillared-pcu SNU-8X, the three most common topologies of MOFs built from the organic linker p,p’-terphenyldicarboxylic acid (tpdc). To synthesize the four squaramide-based MOFs, we designed and synthesized a linker, 4,4’-((3,4-dioxocyclobut-1-ene-1,2-diyl)bis(azanedyil))dibenzoic acid (Sq_tpdc), which is identical in directionality and length to tpdc but which contains organocatalytic squaramide centers. Squaramides were chosen because their immobilization into a framework enhances its reactivity and stability while avoiding any self-quenching phenomena. Therefore, the four MOFs share the same organocatalytic squaramide moiety, but confine it within distinct pore environments. We then evaluated these MOFs as heterogeneous H-bonding catalysts in organic transformations: a Friedel-Crafts alkylation and an epoxide ring-opening. Some of them exhibited good performance in both reactions but all showed distinct catalytic profiles that reflect their structural differences.