Two-dimensional covalent organic frameworks often π stack into crystalline solids that allow precise spatial positioning of molecular building blocks. Inspired by the hydrogen-bonded G-quadruplexes found frequently in guanine-rich DNA, here we show that this structural motif can be exploited to guide the self-assembly of naphthalene diimide and perylene diimide electron acceptors end-capped with two guanine electron donors into crystalline G-quadruplex-based organic frameworks, wherein the electron donors and acceptors form ordered, segregated π-stacked arrays. Time-resolved optical and electron paramagnetic resonance spectroscopies show that photogenerated holes and electrons in the frameworks have long lifetimes and display recombination kinetics typical of dissociated charge carriers. Moreover, the reduced acceptors form polarons in which the electron is shared over several molecules. The G-quadruplex frameworks also demonstrate potential as cathode materials in Li-ion batteries because of the favourable electron- and Li-ion-transporting capacity provided by the ordered rylene diimide arrays and G-quadruplex structures, respectively.