The Eurasian red squirrel 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 examined 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 model-forest design plan development process to assess four felling and restock scenarios to help improve red squirrel population viability. Overall extinction in both forest systems was rare, but high in Uswayford (84%). Survival could be drastically increased (from 16 - 70%) by felling and restocking adjustments, and improving dispersal between the two adjacent forests. The process has been an exemplar of how modelling can have a direct input to land management to help managers objectively balance the differing pressures of multipurpose forestry.