The coexistence of distinct metallic and insulating electronic phases within the same sample of a perovskite manganite, such as La1-x-yPryCaxMnO3, presents researchers with a tool for tuning the electronic properties in materials. In particular, colossal magnetoresistance in these materials-the dramatic reduction of resistivity in a magnetic field-is closely related to the observed texture owing to nanometre- and micrometre-scale inhomogeneities. Despite accumulated data from various high-resolution probes, a theoretical understanding for the existence of such inhomogeneities has been lacking. Mechanisms invoked so far, usually based on electronic mechanisms and chemical disorder, have been inadequate to describe the multiscale, multiphase coexistence within a unified picture. Moreover, lattice distortions and long-range strains are known to be important in the manganites. Here we show that the texturing can be due to the intrinsic complexity of a system with strong coupling between the electronic and elastic degrees of freedom. This leads to local energetically favourable configurations and provides a natural mechanism for the self-organized inhomogeneities over both nanometre and micrometre scales. The framework provides a physical understanding of various experimental results and a basis for engineering nanoscale patterns of metallic and insulating phases.