Context <p>The isomerization of substituted cyclopentadienyl systems plays an important role in understanding substituent effects on sigmatropic rearrangements and proton transfer processes. In this work, R- and proton-shifts in substituted cyclopentadienes (MeCp, tBuCp, SiMe₃Cp, NO₂Cp, and NH₂) were systematically investigated. The R-shift proceeds via a single-step pathway, with the nature of the interaction between the migrating group and the ring strongly dependent on the substituent. For MeCp and NH₂Cp, the migrating group remains covalently bound throughout the process, whereas bulky and electron-withdrawing substituents (tBu, SiMe₃, NO₂) lead to polarized transition states with partial charge separation and elongated bonds. Activation barriers are moderate to high, with the lowest values observed for SiMe₃Cp, and all reactions are exergonic. Proton migration follows a consistent non-classical mechanism involving a transient trisynaptic V(C,C,H) basin and formation of a new C–H bond without full proton dissociation. Substituents primarily influence the extent of electronic reorganization, with NO₂ inducing increased asynchronicity, while the overall mechanism remains preserved. All processes can be formally classified as [1,5]-sigmatropic rearrangements.</p> Methods <p>All calculations were performed using the Gaussian 16 software package. Geometry optimizations and energy calculations were carried out at the ωB97X-D/6-311+G(d,p) level of theory. Solvent effects (toluene, acetone, nitromethane) were included using the PCM model. Transition states were located using the QST2 method and verified by frequency analysis and intrinsic reaction coordinate (IRC) calculations. Topological analyses of the electron localization function (ELF) were performed with TopMod 09 along the IRC, forming the basis for Bond Evolution Theory (BET) analysis. QTAIM analyses were conducted using the Multiwfn program.</p>