Brachyuran crabs are ecologically and economically important macrofauna in mangrove habitats. However, they are exposed to various contaminants, including plastics, which bioaccumulate in relation to their feeding modes. Setiu Wetlands is a unique place on the east coast of Peninsular Malaysia where different ecosystems such as mangroves, lagoon, beaches, etc., are duly connected and influencing each other. In recent years, the shifted river mouth has threatened these wetlands, causing severe hydrodynamic changes in the lagoon, especially in the core mangrove zone. The present study tested microplastics (MPs) contamination in the mangroves through brachyuran crabs as indicators. Three sampling sites, namely Pulau Layat, Kampung Pengkalan Gelap, and Pulau Sutung were chosen. The four abundant crab species Parasesarma eumolpe, Metaplax elegans, Austruca annulipes, and Scylla olivacea, which display different feeding behaviours were collected from all sites covering the dry (Feb–Mar 2021) and the wet (Dec 2021–Jan 2022) seasonal periods. There were significant differences in the seasonal abundance of MPs among crab species. The highest accumulation of MPs in the crab stomachs in the dry season could be linked to subdued water circulation and poor material dispersion. Besides the lower MPs in the wet period due to improved water exchange conditions, its significant presence in the stomachs of S. olivacea indicates the role of its feeding behaviour as a carnivore. In addition, the micro-Fourier transform infrared spectroscopy (micro-FTIR) revealed the widespread occurrence of polymers such as rayon and polyester in all species across the sites. Given the fact that crabs like S. olivacea are commercially important and the ones contaminated with MPs can cause detrimental effects on the local community's health, further managerial actions are needed to assure sustainable management of the Setiu Wetlands.