Density functional theory calculations show that the $Cp_2M$ in cis-dimetallabicycles of metallacyclopentynes, $Cp_2M[μ-(η^4:η^2-H_2C_4H_2)]M'L_2 (M = Ti, Zr$ and M' Ti, Zr), deviates from the C4 plane. Both the metal fragments deviate from the C4 plane in the nickel complexes of metallacyclopentynes (3Ti-Ni and 3Zr-Ni). The nonplanarity of $Ni(PH_3)_2$ from the C4 plane reduces the antibonding interaction between nickel orbitals and the $π-MO$ at the C2-C3 bond, whereas that of the $Cp_2M$ acts mainly to reduce the antibonding interaction between C1 and C2. The energetics of the isodesmic equations show that the nickel complexes 3Ti-Ni and 3Zr-Ni are more stable than the homodimetallabicycles, 3Zr-Zr and 3Ti-Ti. The electron deficiency on the cis-homodimetallabicycles due to the vacant d-orbital on $η^2-M'$ can be decreased by accepting electrons from a Lewis base or by flipping into trans geometry. This is reflected in the experimental realization of cis-$Cp_2Zr[μ-(η^4:η^2-H_2C_4H_2)]ZrCp_2(PMe_3)$ and the trans geometry for $Cp_2Ti[μ-(η^3:η^3-H_2C_4H_2)]TiCp_2$ and $Cp_2Zr[μ-(η^3:η^3-H_2C_4H_2)]ZrCp_2$.