The linear stability of layered two-phase Poiseuille flows through soft-gel-coated parallel walls is studied in this work. The focus is on determining the effect of the elastohydrodynamic coupling between the fluids and the soft-gel layers on the different instabilities observed in flows between parallel plates. The fluids are assumed Newtonian and incompressible, while the soft gels are modeled as linear viscoelastic solids. A long-wave asymptotic analysis is used to obtain an analytical expression for the growth rate of the disturbances. A Chebyshev collocation method is used to numerically solve the general linearized equations. Three distinct instability modes are identified in the flow: (a) a liquid-liquid long-wave mode; (b) a liquid-liquid short-wave mode; (c) a gel-liquid short-wave mode. The effect of deformability of the soft gels on these three modes is analyzed. From the long-wave analysis of the liquid-liquid mode a stability map is obtained, in which four different regions are clearly demarcated. It is shown that introducing a gel layer near the more viscous fluid has a predominantly stabilizing effect on this mode seen in flows between rigid plates. For parameters where this mode is stable for flow between rigid plates, introducing a gel layer near the less viscous and thinner fluid has a predominantly destabilizing effect. The liquid-liquid short-wave mode is destabilized by the introduction of soft-gel layers. Additional instability modes at the gel-liquid interfaces induced by the deformability of the soft-gel layers are identified. We show that these can be controlled by varying the thickness of the gel layers. Insights into the physical mechanism driving different instabilities are obtained using an energy budget analysis. © 2017 American Physical Society.