Sodium alendronate is a nitrogen-containing bisphosphonate, widely used for osteoporosis treatment. However, due to its several oral administration drawbacks, the transdermal route represents an interesting option. The aim of this study was to formulate sodium alendronate in two submicron delivery systems, microemulsions, and solid-in-oil nanosuspensions, both systems possessing permeation enhancing properties. The composition of microemulsions was determined through the construction of pseudo-ternary phase diagrams. Solid-in-oil nanosuspensions were prepared by an emulsification-freeze-drying method, evaluating the effect of sonication time and the type of surfactant. According to the results of drug loading capacity, droplet/particle size, and polydispersity index, two microemulsions and two nanosuspensions were selected to perform the subsequent evaluations. The results showed that microemulsions allowed a faster release of alendronate than nanosuspensions. The permeation capacity of alendronate formulations was assessed through the synthetic membrane Strat M®, as well as through pigskin, finding higher fluxes with microemulsions than with nanosuspensions. In order to elucidate the effect of the formulations on the permeability barrier of the stratum corneum, techniques such as ATR-FTIR and TEWL were used. Finally, measurements of erythema intensity showed that neither of the two nanosystems caused skin irritation after 2 hours of contact. The results suggest that alendronate formulated in a microemulsion can be a viable transdermal nanocarrier for osteoporosis treatment.Copyright © 2020. Published by Elsevier B.V.