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This work presents a novel approach to finely tune experimentally the miscibility and morphological features of ternary high-performance polymer systems composed of poly(ether ether ketone) (PEEK) and two isomeric forms of poly(ether imide) (PEI), meta-PEI (m-PEI) and para-PEI (p-PEI). By controlling the PEEK, m-PEI (miscible with PEEK) and p-PEI (partially miscible with PEEK) compositions, processing parameters, and thermal history, it is possible to control the level of miscibility of the system, and the resulting microstructural length scale over nearly 4 orders of magnitude─from the nanometer scale for fully homogeneous systems, to tens of micrometers for phase-separated cocontinuous networks, without relying on any interfacial compatibilizer. Interestingly, the morphologies of shear-induced homogeneous states are observed and undergo phase separation upon thermal annealing─a phenomenon seldom reported. To understand the resulting phase diagram, binary Flory–Huggins segmental interaction parameters (χij) were calculated from experimental calorimetric data for all three polymer pairs, including two new systems not reported previously in the literature, i.e., PEEK/p-PEI and m-PEI/p-PEI. Based on these parameters, a spinodal decomposition curve was computed, which compares relatively well to the experimental ternary phase diagram. The resulting phase diagram not only offers predictive power for material design but also provides valuable insights into the subtle interplay between structural isomerism and blend miscibility in these high-performance polymer systems. Finally, by selectively extracting both PEIs, porous PEEK monolithic materials can be generated displaying fully interconnected porosities, tunable from a few nanometers to several micrometers in size. This could potentially impact fields encompassing filtration and separation processes, to biomedical material design.