An explicit expression of the generating functional of two-flavor low-energy QCD with external sources in the presence of non-vanishing nucleon densities has been derived recently [1]. Within this approach we derive power counting rules for the calculation of in-medium pion properties. We develop the socalled standard rules for residual nucleon energies of the order of the pion mass and a modified scheme (non-standard counting) for vanishing residual nucleon energies. We also establish the different scales for the range of applicability of this perturbative expansion, which are √ 6πf π ≃ 0.7 GeV for the standard and 6π 2 f 2 π /2m N ≃ 0.27 GeV for non-standard counting, respectively. We have performed a systematic analysis of n-point in-medium Green functions up to and including next-to-leading order when the standard rules apply. These include the in-medium contributions to quark condensates, pion propagators, pion masses and couplings of the axial-vector, vector and pseudoscalar currents to pions. In particular, we find a mass shift for negatively charged pions in heavy nuclei that agrees with recent determinations from deeply bound pionic 207 Pb. We have also established the absence of in-medium renormalization in the π 0 → γγ decay amplitude up to the same order. The study of ππ scattering requires the use of the non-standard counting and the calculation is done at leading order. Even at that order we establish new contributions not considered so far. We also point towards further possible improvements of this scheme and touch upon its relation to more conventional many-body approaches.