A series of 19 ionic liquids (ILs) based on phosphonium and imidazolium cations of varying alkyl‐chain lengths with the orthoborate anions bis(oxalato)borate [BOB]−, bis(mandelato)borate, [BMB]− and bis(salicylato)borate, [BScB]−, are synthesized and studied using small‐angle neutron scattering (SANS). All measured systems display nanostructuring, with 1‐methyl‐3‐n‐alkyl imidazolium‐orthoborates forming clearly bicontinuous L3 spongelike phases when the alkyl chains are longer than C6 (hexyl). L3 phases are fitted using the Teubner and Strey model, and diffusely‐nanostructured systems are primarily fitted using the Ornstein‐Zernicke correlation length model. Strongly‐nanostructured systems have a strong dependence on the cation, with molecular architecture variation explored to determine the driving forces for self‐assembly. The ability to form well‐defined complex phases is effectively extinguished in several ways: methylation of the most acidic imidazolium ring proton, replacing the imidazolium 3‐methyl group with a longer hydrocarbon chain, substitution of [BOB]− by [BMB]−, or exchanging the imidazolium for phosphonium systems, irrespective of phosphonium architecture. The results suggest there is only a small window of opportunity, in terms of molecular amphiphilicity and cation:anion volume matching, for the formation of stable extensive bicontinuous domains in pure bulk orthoborate‐based ILs. Particularly important for self‐assembly processes appear to be the ability to form H‐bonding networks, which offer additional versatility in imidazolium systems.