This paper considers the numerical treatment of the time-dependent Gross–Pitaevskii equation. In order to conserve the time invariants of the equation as accurately as possible, we propose a Crank–Nicolson-type time discretization that is combined with a suitable generalized finite element discretization in space. The space discretization is based on the technique of Localized Orthogonal Decompositions and allows to capture the time invariants with an accuracy of order O ( H 6 ) \mathcal {O}(H^6) with respect to the chosen mesh size H H . This accuracy is preserved due to the conservation properties of the time stepping method. Furthermore, we prove that the resulting scheme approximates the exact solution in the L ∞ ( L 2 ) L^{\infty }(L^2) -norm with order O ( τ 2 + H 4 ) \mathcal {O}(\tau ^2 + H^4) , where τ \tau denotes the step size. The computational efficiency of the method is demonstrated in numerical experiments for a benchmark problem with known exact solution.