Retention of amphiphilic protein activity within the lipid bilayer membrane of the nanostructured biomimetic bicontinuous cubic phase is crucial for applications utilizing these hybrid protein–lipid self-assembly materials, such as in meso membrane protein crystallization and drug delivery. Previous work, mainly on soluble and membrane-associated enzymes, has shown that enzyme activity may be modified when immobilized, including membrane bound enzymes. The effect on activity may be even greater for amphiphilic enzymes with a large hydrophilic domain, such as the Neisserial enzyme lipid A phosphoethanolamine transferase (EptA). Encapsulation within the biomimetic but non-endogenous lipid bilayer membrane environment may modify the enzyme conformation, while confinement of the large hydrophilic domain with the nanoscale water channels of a continuous lipid bilayer structure may prevent full function of this enzyme. Herein we show that NmEptA remains active despite encapsulation within a nanostructured bicontinuous cubic phase. Full transfer of the phosphoethanolamine (PEA) group from a 1,2-dioleoyl-glycero-phosphoethanolamine (DOPE) doped lipid to monoolein (MO), which makes up the bicontinuous cubic phase, is shown. The reaction was found to be non-specific to the alkyl chain identity. The observed rate of enzyme activity is similar to other membrane bound enzymes, with complete transfer of the PEA group occurring in vitro, under the conditions studied, over a 24 hour timescale.