The synthesis of methyl isobutyl ketone (MIBK) can be carried out by the condensation of acetone in the presence of hydrogen over a supported metal catalyst. Previous studies have shown that hydroxyapatite is an excellent catalyst for condensation reactions. The present investigation was undertaken in order to elucidate the reaction mechanism and site requirements for acetone coupling to MIBK over a physical mixture of hydroxyapatite and Pd/SiO2. The reaction is found to proceed by consecutive aldol addition to form diacetone alcohol (DAA), dehydration of DAA to mesityl oxide (MO), and hydrogenation of MO to MIBK. The products formed by feeding DAA and MO reveal that aldol addition of acetone is rapid and reversible, and that the subsequent dehydration of DAA is rate-limiting. Pyridine and CO2 titration show that aldol dehydration occurs over basic sites via an E1cB mechanism. A series of cation-substituted hydroxyapatite samples were prepared by ion-exchange to further investigate the role of acid-base strength on catalyst performance. Characterization of these samples by PXRD, BET, ICP-OES, XPS, CO2-TPD, and Raman spectroscopy demonstrated that the exchange procedure used does not affect the bulk properties of hydroxyapatite. DFT calculations reveal that in addition to affecting the Lewis acidity/basicity of the support, the size of the cation plays a significant role in the chemistry: cations that are too large (Ba2+) or too small (Mg2+) adversely affect reaction rates due to excessive stabilization of intermediate species. Strontium-exchanged hydroxyapatite was found to be the most active catalyst because it promoted α-hydrogen abstraction and C–O bond cleavage of DAA efficiently.