This study considers the linear stability of Poiseuille-Rayleigh-Bénard flows subjected to a transverse magnetic field, to understand the instabilities that arise from the complex interaction between the effects of shear, thermal stratification, and magnetic damping. This fundamental study is motivated in part by the desire to enhance heat transfer in the blanket ducts of nuclear fusion reactors. In pure magnetohydrodynamic flows, the imposed transverse magnetic field causes the flow to become quasi-two-dimensional and exhibit disturbances that are localized to the horizontal walls. However, the vertical temperature stratification in Rayleigh-Bénard flows feature convection cells that occupy the interior region, and therefore the addition of this aspect provides an interesting point for investigation. The linearized governing equations are described by the quasi-two-dimensional model proposed by Sommeria and Moreau [J. Fluid Mech. 118, 507 (1982)], which incorporates a Hartmann friction term, and the base flows are considered fully developed and one-dimensional. The neutral stability curves for critical Reynolds and Rayleigh numbers, Re c and Ra c, respectively, as functions of Hartmann friction parameter H have been obtained over 10−2 ≤ H ≤ 104. Asymptotic trends are observed as H → ∞ following Re c ∝ H 1/2 and Ra c ∝ H. The linear stability analysis reveals multiple instabilities which alter the flow both within the Shercliff boundary layers and the interior flow, with structures consistent with features from plane Poiseuille and Rayleigh-Bénard flows.