Significance Mevalonate is a building block of archaeal lipids. Three enzymes are involved in its biosynthesis: acetoacetyl-CoA thiolase (thiolase), 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGCS), and HMG-CoA reductase. The thiolase reaction is highly endergonic, which means that archaea have to find a way to overcome this low-flux bottleneck. Our work revealed the presence of a thiolase/HMGCS complex, which directly couples the endergonic thiolase reaction to the exergonic HMGCS reaction. An unexpected third protein spatially connects the thiolase and HMGCS. Strikingly, these two enzymes share the same substrate-binding site. Genomic information indicated that the presence of a thiolase/HMGCS complex is common in most of archaea and many bacteria. Such a natural intermediate-channeling system could lead to new strategies to improve biotechnological mevalonate synthesis.