Fatigue induced subchondral bone (SCB) injury is common in racehorses. Understanding how SCB microstructure and microdamage influence mechanical properties is important for developing injury prevention strategies. We aimed to investigate the properties of equine SCB from three metacarpophalangeal joint sites: the disto-palmar third metacarpal condyle (MCIII), disto-dorsal MCIII and proximal sesamoid bone. Superficial and deeper 2 mm regions of interest were compared within each specimen. Cartilage-bone specimens were analyzed with microCT, then loaded in cyclic compression. Digital image correlation determined local strains. Specimens were stained with lead-uranyl acetate to quantify microdamage. The dorsal MCIII SCB had lower bone volume fraction (BVTV), bone mineral density (BMD), and stiffness compared to the palmar MCIII and sesamoid bone. Superficial SCB had higher BVTV and lower BMD than deeper SCB, except at the palmar MCIII where there was no difference in BVTV between depths. Deep bone was always stiffer than superficial, although the gradient between layers was smaller dorsally. Energy loss was greater superficially in palmar MCIII and sesamoid specimens. Energy loss decreased with cyclic loading in superficial and deep layers of the bone, whereas stiffness remained unchanged. Unconfined compression and end artefacts may have contributed to initial changes in stiffness and hysteresis. Surface staining complicated volumetric microdamage quantification. Superficial equine SCB is uniformly less stiff than deeper bone despite non-uniform differences in bone density and microdamage. This compliant superficial layer has an important role in energy dissipation, but whether it is a specific adaptation or a result of microdamage accumulation is not clear.