In this work we study statistical properties of graph-based clustering algorithms that rely on the optimization of balanced graph cuts, the main example being the optimization of Cheeger cuts. We consider proximity graphs built from data sampled from an underlying distribution supported on a generic smooth compact manifold $M$. In this setting, we obtain high probability convergence rates for both the Cheeger constant and the associated Cheeger cuts towards their continuum counterparts. The key technical tools are careful estimates of interpolation operators which lift empirical Cheeger cuts to the continuum, as well as continuum stability estimates for isoperimetric problems. To our knowledge the quantitative estimates obtained here are the first of their kind.