The geometrical Kosambi–Cartan–Chern approach has been applied to study the systems of differential equations which arise in quantum-mechanical problems of a particle on the background of non-Euclidean geometry. We calculate the geometrical invariants for the radial system of differential equations arising for electromagnetic and spinor fields on the background of the Schwarzschild spacetime. Because the second invariant is associated with the Jacobi field for geodesics deviation, we analyze its behavior in the vicinity of physically meaningful singular points r = M, ∞. We demonstrate that near the Schwarzschild horizon r = M the Jacobi instability exists and geodesics diverge for both considered problems.