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While variations in sedimentary organic matter (OM) quantity, biochemical composition and nutritional quality as well as in meiofaunal abundance and assemblage composition at the macro- and mesoscale are relatively well known, information about variations at the microscale is much scarcer. To shed some light on this issue, we tested the null hypothesis by which abundance and composition of the meiofaunal assemblages, and the quantity, biochemical composition and nutritional quality of sedimentary organic matter in coastal shallow environments do not vary within a frame of 1 m2. No significant variation within the frame emerged for OM quantity, nutritional quality, biochemical composition and the abundance of meiofaunal assemblages. On the other hand, the composition of meiofaunal assemblages varied significantly within the frame and exhibited a clear segregation of assemblages farther to the shore, as a likely result of local micro-hydrodynamic conditions. Spatial autocorrelation analysis revealed that lipid and protein sedimentary contents had a random distribution, whereas carbohydrate and biopolymeric C contents and meiofaunal total abundance were characterized by a patchy distribution, with discrete peaks within the sub-frame squares (ca. 0.1 m2). Phytopigments showed a spatial positive autocorrelation distribution, following the micro-hydrodynamic pattern, with patches larger than the sub-frame square, but smaller than the entire one (1 m2). Overall, our results suggest that, within 1 m2 of subtidal sandy sediments, three replicates could be sufficient to assess correctly OM attributes and the abundance of meiofauna, but could be possibly inadequate for assessing meiofaunal assemblages’ composition at a finer scale (<1 m2).