While a number of approaches toward multicomponent metal-organic frameworks have been reported, new strategies affording greater structural versatility and molecular precision are needed to replicate the sophisticated active sites found in enzymes. Here, we outline a general method for templating functional groups within framework pores using thermolabile ligand cross-linkers. We show that tertiary ester-based cross-linkers can be used to install well-defined carboxylic acid pairs at precise relative distances and orientations. The tertiary ester linkages remain intact during framework formation but are readily cleaved to reveal free carboxylic acids upon microwave heating. Successful cross-linker synthesis, framework incorporation, and thermolysis is demonstrated using the mesoporous, terphenyl expanded analogues of MOF-74. When short cross-linkers are used, modeling studies show that the carboxylic acids are installed in a single configuration down the pore channels, spaced ∼7 Å apart. These precisely positioned acid pairs can be used as synthetic handles to build up more complex cooperative active sites.