The dataset is based on 50 soft carbonate sediment samples from the reef island Barrang Lompo in the Spermonde Archipelago, Sulawesi, SE Asia. The subsurface samples were obtained by percussion drilling at 5 coring locations on the island. From each coring location, 10 samples were retrieved in 1 m intervals, thus providing samples from a maximum depth of 10 m below surface at each site (1 m, 2 m, ..., 10 m). Laboratory data was collected between 2019 and 2021. The provided dataset contains skeletal component analysis (counting of fragments, 500 per sample; raw data). Microscope analysis of 200 components from fractions >2 mm and 2-1 mm and 100 components from fraction 1-0.5 mm. 12 different calcifying organisms were distinguished, of which 10 were identified in the present dataset. Non-identifiable grains were counted as bioclasts and not added to the sum of 200 and 100, respectively.The collected data provides information of reef-derived sedimentation in the Holocene in the Spermonde Archipelago. It provides insight into the ecological background and the origin of the skeletal sediments.