Given an axially-symmetric, \((n+1)\) -dimensional convex cone \(\Omega \subset \mathbb {R}^{n+1}\) , we study the stability of the free-boundary minimal surface \(\Sigma \) obtained by intersecting \(\Omega \) with a n-plane that contains the axis of \(\Omega \) . In the case \(n=2\) , \(\Sigma \) is always unstable, as a special case of the vertex-skipping property that we recently proved in another article. Conversely, as soon as \(n\ge 3\) and \(\Omega \) has a sufficiently large aperture (depending on the dimension n), we show that \(\Sigma \) is strictly stable. For our stability analysis, we introduce a Lipschitz flow \(\Sigma _{t}[f]\) of deformations of \(\Sigma \) associated with a compactly-supported, scalar deformation field f, which satisfies the key property \(\partial \Sigma _{t}[f] \subset \partial \Omega \) for all \(t\in \mathbb {R}\) . Then, we compute the lower-right second variation of the area of \(\Sigma \) along the flow, and ultimately show that it is positive by exploiting its connection with a functional inequality studied in the context of reaction-diffusion problems.