Structured optimization problems are ubiquitous in fields like data science and engineering. The goal in structured optimization is using a prescribed set of points, called atoms, to build up a solution that minimizes or maximizes a given function. In the present paper, we want to minimize a black-box function over the convex hull of a given set of atoms, a problem that can be used to model a number of real-world applications. We focus on problems whose solutions are sparse, i.e., solutions that can be obtained as a proper convex combination of just a few atoms in the set, and propose a suitable derivative-free inner approximation approach that nicely exploits the structure of the given problem. This enables us to properly handle the dimensionality issues usually connected with derivative-free algorithms, thus getting a method that scales well in terms of both the dimension of the problem and the number of atoms. We analyze global convergence to stationary points. Moreover, we show that, under suitable assumptions, the proposed algorithm identifies a specific subset of atoms with zero weight in the final solution after finitely many iterations. Finally, we report numerical results showing the effectiveness of the proposed method.