The electron-rich isomeric complexes CpMo(η3-C3H5)(η4-C4H6) (1a, prone-C3H5; supine-C4H6; 1b, supine-C3H5; supine-C4H6; 1c, supine-C3H5; s-trans-C4H6) do not react with neutral ligands under mild conditions. They are, however, easily protonated by a variety of different acids. Protonation of 1a and 1b involves attack at the terminal position of the allyl ligand and elimination of propene. Protonations with acetic acid show rates in the order 1a > 1b and afford the same product, CpMo(O2CCH3)(η4-C4H6), 2, which can be oxidized to the 17-electron cation [2]+. HBF4 protonation of 1a in the absence of trapping donor molecules affords [CpMo(η4-supine-C4H6)(μ-F2BF2)]n, 3. The latter readily reacts with donor molecules to afford [CpMo(η4-supine-C4H6)L2][BF4] products (L = MeCN, 4; ButNC, 5; or L2 = 1,3-butadiene, 6), which are also directly and selectively obtained by protonation of 1a in the presence of the appropriate ligand. Compound 6 has a (supine-C4H6)(s-trans-C4H6) configuration and converts into compound 4 when dissolved in MeCN. Protonation of 1c is much slower relative to the isomers 1a and 1b. The observed products depend on the nature of the solvent. Protonation by HBF4·Et2O in MeCN affords unstable [CpMo(supine-η-C3H5)(syn-CH3-prone-η-C3H4)(NCCH3)][BF4] (7), which rapidly exchanges the MeCN ligand. Decomposition of the latter involves a regioselective reductive coupling of the two allyl ligands to generate 3-methyl-1,5-hexadiene quantitatively. In C6D6, the HBF4 protonation of 1c produces small amounts of propene and a violet precipitate which gives a mixture of 4 and 7 upon treatment in MeCN. In the presence of 1,3-butadiene, protonation of 1c in THF followed by extraction into acetone affords a mixture of 6 and [CpMo(η-C3H4-CH2CH2-η-C3H4)(Me2CO)][BF4] (8). Compound 8 converts into [CpMo(η-C3H4-CH2CH2-η-C3H4)(L)][BF4] (L = MeCN, 9; PMe3, 10) when treated with the appropriate L. Protonation of 1c in MeCN in the presence of butadiene affords 7 which slowly decomposes, under these conditions, to a mixture of 4 and [CpMo(η4-s-trans-C4H6)(MeCN)2]+, 11. The collective results for the protonation of 1c indicate that the proton attacks the s-trans diene ligand in MeCN. The preferred position of attack in nonpolar solvents, on the other hand, is the allyl. The difference of electronic distribution for isomers 1a−c has been investigated by DFT methods. The calculations indicate that the allyl ligand is a stronger donor in the supine configuration, while the diene ligand is both a weaker donor and a weaker acceptor when it is coordinated in the s-trans mode.