Alkanes are known to promote the fluid lamellar (Lα)-to-inverted hexagonal (HII) phase transition of different phospholipids. In this work, we studied the interaction of decane and tetradecane with self-assemblies formed of 1-palmitoyl-2-oleoyl-sn-glycero-phosphoethanolamine (POPE), using sequential 2H and 31P solid-state NMR spectroscopy. This technique allowed calculating the partitioning constant of the alkanes between the Lα and HII phases of POPE. Our results show that both alkanes are preferentially distributed in the HII phase compared to the Lα phase. In the HII phase, both alkanes display a very high conformational disorder, consistent with their location in the intercylinder voids. This preferential partitioning in the HII phase is more pronounced for tetradecane than for decane. This finding is proposed to be associated with a less energetically favored insertion (limited solubility) of tetradecane in the lamellar phase. This proposition is supported by the observation that tetradecane experiences more conformational freedom than its shorter analog in POPE bilayers, suggesting that it is located, on average, closer to the middle of the bilayers. It is also established that the increase in size of the intercylinder voids, by the addition of 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) in the HII cylinders, enhances the partitioning of decane in the HII phase compared to the Lα phase. These findings propose handles to modulate the balance of the relative Lα/HII phase stability.