A microwave shares a nonintuitive phase called the geometric phase with an interacting electron spin after an elastic scattering. The geometric phase, generally discarded as a global phase, allows universal holonomic gating of an ideal logical qubit, which we call a geometric spin qubit, defined in the degenerate subspace of the triplet spin qutrit. We here experimentally demonstrate nonadiabatic and non-abelian holonomic quantum gates over the geometric spin qubit on an electron or nitrogen nucleus. We manipulate purely the geometric phase with a polarised microwave in a nitrogen-vacancy centre in diamond under a zero-magnetic field at room temperature. We also demonstrate a two-qubit holonomic gate to show universality by manipulating the electron-nucleus entanglement. The universal holonomic gates enable fast and fault-tolerant manipulation for realising quantum repeaters interfacing between universal quantum computers and secure communication networks.