A spatially explicit mathematical model was developed to assess the population viability of red squirrels (Sciurus vulgaris) in designated forest strongholds in Scotland under the implementation of two forest management policies: a specific Stronghold Management for red squirrel conservation (SM) compared to the multi-purpose UK Forestry Standard (UKFS) for sustainable forest management. The study showed that, in the presence of grey squirrels (Sciurus carolinensis), the SM policy provides an advantage to red squirrels over grey squirrels when compared to the UKFS, and its implementation supports red squirrel conservation efforts. When grey squirrels are not present, there is no discernible benefit in the SM policy compared to the UKFS. The model results therefore indicate that species-specific forest management for red squirrel conservation in the absence of sympatric grey squirrels would not be required. This would allow less prescriptive forest management options that maintain viable red squirrel populations to be explored. The study also identified forest regions that, due to their composition, are capable of sustaining a viable red squirrel population, in the presence of grey squirrels, without the application of specific forest management policy. They can be considered ‘natural strongholds’. Selecting such natural strongholds may afford more flexibility to conserve red squirrel populations whilst simultaneously delivering other multi-species conservation and forest management objectives. We review our findings in terms of criteria that were used in the original stronghold designation in Scotland and discuss how our work can be used to inform a forthcoming review of stronghold management policy by Scottish Forestry. Furthermore, the findings can inform red squirrel conservation strategies in other regions and the modelling techniques can be adapted to a wide range of conservation settings.