The growing global threat of antimicrobial resistance, combined with the slowed development of novel antibiotics, has resulted in a critical need for new antimicrobial therapies. Naturally occurring antimicrobial peptides (AMPs) can act as highly potent, broad-spectrum antibiotics which may be less likely to engender resistance in target organisms. However, their susceptibility to proteolysis and lack of specificity necessitates the use of a drug delivery vehicle to both protect the AMP from chemical degradation and provide a platform for further functionalization, enabling the development of targeted delivery and release systems. In this study, we have used lipid-based inverse bicontinuous cubic phase nanoparticles (cubosomes) as delivery vehicles for six different antimicrobial peptides. The phase stability, morphology, and peptide loading efficiency of the nanoparticles were characterized and rationalized according to lipid composition, buffer conditions, as well as peptide charge and hydrophobicity. The AMP loading efficiency within cubosomes was increased significantly through simple manipulation of electrostatic charge. Minimum inhibitory concentration (MIC) values were determined for formulations with high loading efficiency against Staphylococcus aureus, Bacilus cereus, Escherichia coli, and Pseudomonas aeruginosa. Encapsulation within a lipid nanocarrier was shown to increase antimicrobial activity for some formulations. We anticipate that the further development of these peptide loaded cubosomes will enable the design of potent and targeted antibiotic therapies.