The Maldivian archipelago comprises some of the most characteristic and significant world atoll systems, but the meiobenthic assemblages of these islands continue to be largely unknown. To investigate variations in meiofaunal spatial distribution and biodiversity in back-reef platforms, three transects were studied, two at Felidhoo (the north and east sides) and one at South Malé. The sedimentological features of the samples obtained were also analyzed to further current knowledge on the relationships that exist between sediments and meiofauna. Our results reveal that the meiofaunal assemblage at these locations is well diversified and includes 20 major taxa. Nematodes and copepods are dominant, together forming 68% of the total meiofauna, followed by platyhelminthes, polychaetes and ostracods. The nematode assemblage is very rich and composed of 34 families and 123 genera – 96 of which (78%) set new records for the Maldives. The structures of the meiofaunal and nematode assemblages are relatively similar on the ‘large-scale’ level (i.e. when the different platforms are compared) and reveal a low β-diversity. However, significant dissimilarities were detected within each platform, emphasizing that such ‘small-scale’ differences are the main factors determining the structure of the meiofauna and, in particular, the nematode assemblages. Although significant differences were not detected between the transects, greater levels of dissimilarity were recognized at North Felidhoo. Here, the building of inclined deposit layers plays a significant role in increasing the heterogeneity of the platform habitats and sediments, confirming the great importance of sediment granulometry as an environmental variable. Indeed, a close relationship is observed between meiofauna (especially for the nematodes) and grain size, which appears to control the structure, diversity and trophic composition of the Maldivian meiofauna assemblages, thus highlighting the high biodiversity existing in the medium-coarse sands.