In this work, the effects of slip velocity on the flow and heat transfer for an electrically conducting micropolar fluid over a permeable stretching surface with variable heat flux in the presence of heat generation (absorption) and a transverse magnetic field are investigated. The governing partial differential equations describing the problem are converted to a system of non-linear ordinary differential equations by using the similarity transformation, which is solved numerically using the Chebyshev spectral method. The effects of the slip parameter on the flow, micro-rotation and temperature profiles as well as on the local skin-friction coefficient, the wall couple stress and the local Nusselt number are presented graphically. The numerical results of the local skin-friction coefficient, the wall couple stress and the local Nusselt number are given in a tabular form and discussed.