Energy functionals produced by second-order homogenization of periodic elastic structures commonly feature negative gradient moduli. We show that this undesirable property is caused by the truncation of the energy expansion in powers of the small scale separation parameter. By revisiting Cholesky's LDLT decomposition, we propose an alternative truncation method that restores positivity while preserving the order of accuracy. We illustrate this method on a variety of periodic structures, both continuous and discrete, and derive compact analytical expressions of the homogenized energy that are positive and accurate to second order. The method can also cure the energy functionals produced by second-order dimension reduction, which suffer similar non-positivity issues. It naturally extends beyond second order.