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The CNOT gate is a two-qubit gate which is essential for universal quantum computation. A well-established approach to implement it within Majorana-based qubits relies on subsequent measurement of (joint) Majorana parities. We propose an alternative scheme which operates a protected CNOT gate via the holonomic control of a handful of system parameters, without requiring any measurement. We show how the adiabatic tuning of pair-wise couplings between Majoranas can robustly lead to the full entanglement of two qubits, insensitive with respect to small variations in the control of the parameters.