Poly(ether-ether-ketone) has received increased attention due to its high thermal and chemical stability, and high performance in various applications. However, it suffers from semi-crystalline morphology, low fractional free volume, and poor processability, requiring the use of harsh acidic solvents, which leads to undesired sulfonation. In this work, three intrinsically microporous poly(ether-ether-ketone) (iPEEK), incorporating spirobisindane, Tröger’s base, and triptycene contorted structures, were developed for organic solvent nanofiltration. Molecular dynamics simulations have assisted the molecular engineering of the polymers and the understanding of the improved membrane performance through the binding energies between solvents and polymers. Application of the design principles of polymers of intrinsic microporosity has led to a paradigm shift with a notable enhancement in both the polymer properties and the subsequently fabricated nanofiltration membranes’ performance. The iPEEKs showed excellent solution processability, high surface area of 205–250 m2 g-1, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol-1 displaying 2–6 fold higher permeance (3.57–11.09 L m-2 h-1 bar-1) than previous reports. The long-term stabilities were demonstrated by a 7-day continuous cross-flow filtration.