•Low temperature neutron diffraction data reveal non-collinear magnetic structure in Co4Ta2O9.•Neutron diffraction data fit best to a non-centro-symmetric crystal structure below Neel temperature.•Correlation between magnetic structure and improper ferroelectricity is analyzed for Co4Ta2O9.•Co-existing large magnetoelectric coupling is determined in the spin-flop phase of Co4Ta2O9. We study magnetocapacitance (MC) effect and magnetoelectric (ME) coupling in spin-flop driven antiferromagnet Co4Ta2O9. Powder neutron diffraction data reveal that the magnetic structure corresponds to a non-collinear arrangement along with a non-centrosymmetric crystal structure below Néel Temperature. Electric polarization is achieved below Néel temperature only when the sample is cooled in the presence of external magnetic field. The magnetocapacitance data at high magnetic fields are analyzed by phenomenological Ginzburg-landau theory of ferro-electromagnets and it is found that change in dielectric constant is proportional to the square of magnetization. The saturation polarization and magnetoelectric coupling are estimated to be 52 µC/m2 and γ = 1.4 × 10−3 (emu/g)−2 respectively at 6 Tesla. Strong magnetoelectric coupling and ferroelectric phase in the anti-ferromagnetic Co4Ta2O9 are correlated to magnetic structure as derived from neutron diffraction data.