Modelling the spatial distribution of multi-habitat species is challenging since they show multi-dimensional environmental responses that may vary sharply through habitats. Hence, for these species, the achievement of realistic models useful in conservation planning may depend on the appropriate consideration of habitat information in model calibration. We aimed to evaluate the role of different types of habitat predictors, along with habitat-partitioning, to improve model inference, detect non-stationary responses across habitats and simulate the impact of sampling bias on spatial predictions. As a case study, we modelled the occurrence of the multi-habitat plant species bilberry (Vaccinium myrtillus) in the Cantabrian Mountains (NW Spain), where it represents a basic trophic resource for threatened brown bear and capercaillie.We used MaxEnt to compare a baseline model approach calibrated with topo-climatic variables against three alternative approaches using explicit habitat information based on vegetation maps and remote sensing data. For each approach, we ran non-partitioned (all habitats together) and habitat-partitioned models (one per habitat) and evaluated model performance, overfitting and extrapolation. The highest performance was for habitat-partitioned models including habitat predictors. The lowest overfitting was for the baseline non-partitioned model, at the cost of achieving the highest predicted fractional area. The extrapolation success of habitat-partitioned models was low, with the highest performance for the baseline approach. Our results highlight that multihabitat species responses are non-stationary across habitats, with habitat-biased data resulting in weak spatial predictions. When modelling the distribution of multi-habitat species at regional scale, we recommend using habitat-partitioned models including habitat predictors, either vegetation maps or remote sensing data, to improve the realism of spatial outputs and its applicability in regional conservation planning.3