We consider an iteration method for solving an elliptic type boundary value problem Au=f, where a positive definite operator A is generated by a quasi-periodic structure with rapidly changing coefficients (a typical period is characterized by a small parameter ϵ). The method is based on using a simpler operator A0 (inversion of A0 is much simpler than inversion of A), which can be viewed as a preconditioner for A. We prove contraction of the iteration method and establish explicit estimates of the contraction factor q. Certainly the value of q depends on the difference between A and A0. For typical quasi-periodic structures, we establish simple relations that suggest an optimal A0 (in a selected set of “simple” structures) and compute the corresponding contraction factor. Further, this allows us to deduce fully computable two-sided a posteriori estimates able to control numerical solutions on any iteration. The method is especially efficient if the coefficients of A admit low-rank representations and if algebraic operations are performed in tensor structured formats. Under moderate assumptions the storage and solution complexity of our approach depends only weakly (merely linear-logarithmically) on the frequency parameter 1/ϵ.