The complexity of mangrove habitats, habitat heterogeneity, and the patchiness of crab assemblages could introduce potential confounding factors that make detection of physical disturbance impacts on mangrove crab assemblages difficult. This study categorized the effects of small-scale disturbance on mangrove crabs by examining changes in crab abundance and species richness in six mangrove sites at Merbok and Penang mangroves, North-west of Peninsular Malaysia across four months. Treatments that represented small-scale disturbance were introduced comprising control (Treatment 0), the removal of pneumatophores and detritus (Treatment 1) and trampling with size 9 boots (Treatment 2). Experimental design comprised of factors sampling Month (n = 4), Forest (n = 6), and Treatment (n = 3), with four plots as replicates. Sampling of mangrove crabs was conducted using a hand catch method. Seventeen species of crabs were identified, belonging to five families comprising Sesarmidae, Varunidae, Dotilidae, Camptandriidae and Ocypodidae. Several species of sesarmid crabs, and Paracleistostoma depressum from the family Camptandriidae were commonly found in all six sites, while some species from other families were found only in specific sites. The crab abundance was greater in Penang than in Merbok, although crab species richness was lower in Penang. Univariate analysis revealed there were significant effects of disturbance treatments in a specific month and forest on the abundance of the crab Paracleistostoma depressum (SNK Month × Forest × Treatment F(30,216)=1.55; p = 0.04). Paracleistostoma depressum was found to be the most abundant in Penang despite the removal of pneumatophores and detritus, with P. depressum abundance negatively correlating with the number of pneumatophores (r = −0.62, p = 0.03) and detrital biomass (r = −0.61, p = 0.03) in the Gurney site in Penang in September 2016. Thus, species-specific responses of crabs to physical disturbance should be analysed in detail to avoid misrepresentations of the role of habitat complexity in providing shelter for crab species.