Setting Favourable Reference Values (FRVs) can assist the definition of the conservation status of a species. FRVs may consider population, habitat, and range. FRVs can indicate a range of values for different parameters, which should allow the long-term persistence of a species/population. We propose a method for the definition of reference values for the habitat (FRV-H or HRV) of breeding bird species. HRV should cover habitat extent and quality, both required to ensure long-term persistence. Extent HRV should express a measure of suitable area, whereas quality HRV could be defined as the range of values for habitat variables known to affect habitat quality. To define an extent HRV, we built species distribution models (SDMs) and set extent HRV as the extent of potentially suitable habitat under a conservative approach. Quality HRV should refer to environmental determinants/correlates of occurrence and breeding success, and should be defined by the identification of the habitat factors affecting occurrence and reproduction. When habitat selection is adaptive, habitat suitability may approximate habitat quality, being correlated with breeding success. In that case, fine-scaled habitat/distribution models may be used to identify determinants/correlates of reproductive output, and such species-habitat relationships may help define quality HRV. We show examples using the Red-backed Shrike Lanius collurio as a model. The use of habitat selection models, which can be made spatially explicit generating distribution models, may assist the definition of both extension and quality HRVs. Species-habitat models can allow the individuation of factors and relative values affecting species occurrence/reproduction (quality HRV), and the definition of the spatial distribution and quantity of potentially suitable habitat (extent HRV). Our approach is one of the possible ones, aiming at finding a “suitable” trade-off between affordable data and scientific precision. HRVs should be used together with population and range FRVs to assess the status of a species/population.