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A fully discrete analysis of the finite element heterogeneous multiscale method for a class of nonlinear elliptic homogenization problems of nonmonotone type is proposed. In contrast to previous results obtained for such problems in dimension $d\leq2$ for the $H^1$ norm and for a semi-discrete formulation [W.E, P. Ming and P. Zhang, J. Amer. Math. Soc. 18 (2005), no. 1, 121–156], we obtain optimal convergence results for dimension $d\leq3$ and for a fully discrete method, which takes into account the microscale discretization. In addition, our results are also valid for quadrilateral finite elements, optimal a-priori error estimates are obtained for the $H^1$ and $L^2$ norms, improved estimates are obtained for the resonance error and the Newton method used to compute the solution is shown to converge. Numerical experiments confirm the theoretical convergence rates and illustrate the behavior of the numerical method for various nonlinear problems.