In this work, we tackle the problem of minimising the Conditional-Value-at-Risk (CVaR) of output quantities of complex differential models with random input data, using gradient-based approaches in combination with the Multi-Level Monte Carlo (MLMC) method. In particular, we consider the framework of multi-level Monte Carlo for parametric expectations and propose modifications of the MLMC estimator, error estimation procedure, and adaptive MLMC parameter selection to ensure the estimation of the CVaR and sensitivities for a given design with a prescribed accuracy. We then propose combining the MLMC framework with an alternating inexact minimisation-gradient descent algorithm, for which we prove exponential convergence in the optimisation iterations under the assumptions of strong convexity and Lipschitz continuity of the gradient of the objective function. We demonstrate the performance of our approach on two numerical examples of practical relevance, which evidence the same optimal asymptotic cost-tolerance behaviour as standard MLMC methods for fixed design computations of output expectations.