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The study of the dynamics of a two-body system in modified gravity constitutes a more complex problem than in Newtonian gravity. Numerical methods are typically needed to solve the equations of geodesics. Despite the complexity of the problem, the study of a two-body system in $f(R)$ gravity leads to a new exciting perspective hinting the right strategy to adopt in order to probe modified gravity. Our results point out some differences between the {\em semiclassical} (Newtonian) approach, and the {\em relativistic} (geodesic) one thus suggesting that the latter represents the best strategy for future tests of modified theories of gravity. { Finally, we have also highlighted the capability of forthcoming observations to serve as smoking gun of modified gravity revealing a departure from GR or further reducing the parameter space of $f(R)$ gravity}. \keywords{$f(R)$ gravity \and binary system \and geodesics \and precession, Comment: 7 Pages, 2 figures. Accepted for publication on The European Physics Journal C