Geochemical tracers incorporated into the skeleton of reef-building corals are ideal proxies for reconstructing environmental parameters of ambient seawater such as temperature and salinity at subseasonal resolution. However, validation concerns of these environmental proxies due to the complex skeleton of some tropical Atlantic corals have hindered such coral-based environmental reconstructions in this region compared to the tropical Pacific. In order to identify complications associated with the complex skeletal architecture of the massive brain coral Diploria strigosa, we performed microsampling experiments along and across individual skeletal elements. We demonstrate that the mesoscale heterogeneity of Sr/Ca, d18O and d13C is a systematic feature of D. strigosa and is linked to different vital effects between skeletal elements. The thecal wall is significantly depleted in Sr, 18O and 13C compared to the adjacent septa and columella and differences between apparent temperature signatures of several degrees are greater for Sr/Ca suggesting that this temperature proxy is more sensitive to skeletal mixing than d18O. Parallel subseasonal microsampling experiments performed along individual skeletal elements of a single corallite of a D. strigosa coral which grew at a rate of 0.65 cm/year allow for investigating potential biases associated with its complex skeletal mesoarchitecture. Highest correlation between Sr/Ca and d18O from skeletal material retrieved from the centre of the thecal wall suggests that microdrilling the theca provides the best environmental signal compared to adjacent microsampling profiles. Moreover, based on monthly-mean climatology, the temperature dependence of Sr/Ca for this profile is comparable to previous calibrations published from faster growing D. strigosa. Based on these results, we conclude that accurate microsampling along the centre of the thecal wall of D. strigosa is a prerequisite for generating robust climate reconstructions from its skeleton.