Injuries to the Lisfranc complex may require surgical fixation, the stability of which may be correlated with bone mineral density (BMD). However, there is limited research on regional BMD variations in the Lisfranc complex. This study used quantitative micro-CT to characterize regional BMD in the four bones (medial cuneiform, intermediate cuneiform, first metatarsal, and second metatarsal) of this complex. Twenty-four cadaveric specimens were imaged with a calibration phantom using micro-CT. Each bone was segmented and divided into eight regions based on an anatomical coordinate system. BMD for each octant was calculated using scan-specific calibration equations and average image intensity. Differences between regions were analyzed using ANOVA with post hoc analysis and differences between groups of four octants in each plane were analyzed with t-tests with significance level α = 0.05. The highest density region in the medial cuneiform was the distal–dorsal–lateral and dorsal regions showed significantly higher BMD than plantar regions. The intermediate cuneiform had the highest density in the distal–dorsal–medial region and the dorsal and medial regions had higher BMD than the plantar and lateral regions, respectively. The densest region of the first metatarsal was the distal–dorsal–lateral and distal regions had significantly higher BMD than proximal regions. In the second metatarsal, the distal–dorsal–medial region had the highest density, and the distal, dorsal, and medial regions had significantly higher BMD than the proximal, plantar, and lateral regions, respectively. The predominant finding was a pattern of increased density in the dorsal bone regions, which may be relevant in the surgical management of Lisfranc injuries.