The Eurasian red squirrel (Sciurus vulgaris) is under threat in the UK from the introduced North American grey squirrel. National measures to save the species include large conifer forest reserves where management encompasses measures to bolster the native species. However, forests are multi-purpose environments and foresters have to balance different timber production, amenity and conservation objectives. We present a mathematical modelling framework that examines the impacts of potential felling and restocking plans for two reserves, Kidland and Uswayford forests, in northern England. In collaboration with forest managers, we employed an iterative process that used the model to assess four forest design plans (felling and restocking scenarios) with the aim of improving red squirrel population viability. Overall, the model predicted that extinction in both forests at the same time was rare, but high in Uswayford (84%) alone. Survival could be drastically increased (from 16 - 70%) by felling and restocking adjustments, and improving dispersal between the two adjacent forests. This study provides an exemplar of how modelling can have a direct input to land management to help managers objectively balance the differing pressures of multipurpose forestry.