This article presents data on the occurrence and distribution of phthalate esters and metals associated with microplastics (MPs) (1–5 mm) collected from four beaches in the tropical Atlantic ecosystems, Nigeria, Gulf of Guinea. Information on microplastics extraction by density flotation with saturated NaCl and polymer identification with attenuated total reflectance infra-red spectroscopy (ATR-FTIR) is also provided. Analysis of six phthalate esters (PAEs) (dimethyl phthalate (DMP), diethyl phthalate (DEP), dibutyl phthalate (DnBP), benzyl butyl phthalate (BBP), di (ethyl hexyl) phthalate (DEHP), and di n-octyl phthalate (DnOP)) associated with the microplastics by performed using Gas chromatography–mass spectroscopy (GC–MS). Metals including Ag, Al, As, B, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, Pb, Sb, Se, Si, Sr, Ti, Tl, V, and Zn were analysed by inductively coupled plasma–optical emission spectrometry (ICP–OES). The data present the separation of microplastics from sediment, extraction with cyclohexane/ethyl acetate (1:1, v/v) and 10% HNO3 for phthalate esters and metals, respectively, and the determination of target analytes concentrations. The compositional distributions of MPs and levels of carcinogenic and toxic metals and phthalate esters are presented. The dataset could be used for the evaluation of ecological risk associated with PAEs in the marine ecosystems.