The Mannich reaction of the zirconium MOF [Zr6O4(OH)4(bdc‐NH2)6] (UiO‐66‐NH2, bdc‐NH2=2‐amino‐1,4‐benzenedicarboxylate) with paraformaldehyde and pyrazole, imidazole or 2‐mercaptoimidazole led to post‐synthetic modification (PSM) through C−N bond formation. The reaction with imidazole (Him) goes to completion whereas those with pyrazole (Hpyz) and 2‐mercaptoimidazole (HimSH) give up to 41 and 36 % conversion, respectively. The BET surface areas for the Mannich products are reduced from that of UiO‐66‐NH2, but the compounds show enhanced selectivity for adsorption of CO2 over N2 at 273 K. The thiol‐containing MOFs adsorb mercury(II) ions from aqueous solution, removing up to 99 %. The Mannich reaction with pyrazole succeeds on [Zn4O(bdc‐NH2)3] (IRMOF‐3), but a similar reaction on [Zn2(bdc‐NH2)2(dabco)] (dabco=1,4‐diazabicyclo[2.2.2]octane) gave [Zn3(bdc‐NH2)1.32(bdc‐NHCH2pyz)1.68(dabco)]⋅2 C7H8 5, whereas the reaction with imidazole gave the expected PSM product. Compound 5 forms via a dissolution–recrystallisation process that is triggered by the “free” pyrazolate nitrogen atom competing with dabco for coordination to the zinc(II) centre. In contrast, the “free” nitrogen atom on the imidazolate is too far away to compete in this way. Mannich reactions on [In(OH)(bdc‐NH2)] (MIL‐68(In)‐NH2) stop after the first step, and the product was identified as [In(OH)(bdc‐NH2)0.41(bdc‐NHCH2OCH3)0.30(bdc‐N=CH2)0.29], with addition of the heterocycle prevented by steric interactions.