Silicon microneedle patches were investigated, alone or in combination with lipid microparticles (LMs), as a system to improve the in vitro skin penetration of the antioxidant flavonoid, quercetin. LMs loaded with quercetin were prepared by melt emulsification and sonication. The flavonoid content of LMs was 11.7 ± 0.3% and their mean diameter and polydispersity index were 8.1 μm and 0.66, respectively. Emulsions containing quercetin, free or microencapsulated, were applied to untreated- or microneedle-treated pig skin mounted in Franz diffusion cells. The amount of flavonoid penetrated into the stratum corneum and viable epidermis were measured by HPLC, after validated tape-stripping and bead mill homogenization procedures, respectively. Compared to intact skin, a marked increase in quercetin levels permeated into the stratum corneum (from 1.19 ± 0.12 μg/cm2 to 2.23 ± 0.54 μg/cm2) and viable epidermis (from 0.10 ± 0.01 μg/cm2 to 0.56 ± 0.27 μg/cm2) was achieved when skin was treated with the flavonoid-loaded LMs in combination with microneedle arrays. Conversely, perforation of the cutaneous surface by microneedles did not produce any significant improvement in the skin penetration of non-encapsulated quercetin. The enhanced (5.5-fold) intra-epidermal delivery of quercetin attained by the LM/microneedle strategy described here, is particularly relevant since the main quercetin site of action is in the epidermis.