We construct a novel estimator for the diffusion coefficient of the limiting homogenized equation, when observing the slow dynamics of a multiscale model, in the case when the slow dynamics are of bounded variation. Previous research suggests subsampling the data on fixed intervals and computing the corresponding quadratic variation. However, to achieve optimality, this approach requires knowledge of scale separation variable $ε$. Instead, we suggest computing the quadratic variation corresponding to the local extrema of the slow process. Our approach results to a natural subsampling and avoids the issue of choosing a subsampling rate. We prove that the estimator is asymptotically unbiased and we numerically demonstrate that its $L_2$-error is of order ${\mathcal O}(ε^2)$.