Three selectively labeled propynes were prepared either with deuterium or carbon‐13 at position 3 and doubly labeled with carbon‐13 at positions 1 and 2 by an alkylation reaction from the corresponding labeled or unlabeled monolithio acetylides and dimethylsulfates. Their lithiation with nBuLi gave the corresponding propynyllithium derivatives which reacted with dimethyl squarate to afford the corresponding propargylic alcohols. These were thermolysed in p‐xylene to furnish [5‐D3‐methyl]‐, [5‐13C‐methyl]‐, and [5,6‐13C2‐2,5‐cyclohexadienyl]ubiquinone. The farnesyl side chain was introduced onto the labeled quinones with farnesyl trimethyltin under BF3 catalysis to provide [5‐D3‐methyl]‐, [5‐13C‐methyl]‐, and [5,6‐13C2‐2,5‐cyclohexadienyl]ubiquinone 3 (6c, 6b, 6a, respectively).