A new formulation for the eddy-diffusivity parameterization of the cloudy boundary layer is presented. The new aspects of the scheme are: (i) two prognostic turbulent kinetic energies (TKE), for the clear and cloudy air; (ii) in each region, the mixing length is formulated in terms of the TKE and a time scale. Additionally a statistical cloud scheme is used. The model is evaluated in a decoupling stratocumulus case and in a cumulus case, using a single-column mode. The model realistically simulates the overall cloud properties. The in-cloud mixing length formulation qualitatively matches the typical eddy size (as diagnosed from large eddy simulations). Consistent interactions between the sub-cloud and the cloud layers are achieved through a realistic in-cloud mixing. In the cumulus case, the conditionally unstable layer is maintained. These results show that boundary layer clouds and associated mixing can be represented consistently in the context of the eddy-diffusivity approach.