Networks of protected areas (PAs) where human activities are allowed at different degrees are fundamental to ensure the long-term conservation of biological diversity and ecological processes. However, studies aimed at assessing their effectiveness, focusing on several species simultaneously are scarce. We assessed the effectiveness of the system of protected areas (PAs) of Lombardy, Northern Italy, in conserving bird populations by comparing the changes from 1992 to 2013 in the occurrence of 54 breeding bird species censused in areas classified in different protection categories, namely Nature Reserves (NRs), areas designed predominantly for the protection of nature; Regional Parks (RPs), naturally valuable areas where human activities, including intensive agriculture, are allowed; and non-protected areas (NPAs). Overall, occurrence of common birds increased in Lombardy in the last 20 years and farmland and long-distance migrants (LDMs), which suffered sharp declines at a continental scale, showed stable and increasing trends, respectively. These trends were, however, the balance between those of species whose occurrence markedly increased, and those of species that dramatically declined. Species occurred more often in PAs than in NPAs, while temporal trends in occurrence were significantly more positive in RPs than in both NRs and NPAs. Hence, PAs seemed effective in preserving common bird communities. Occurrence of woodland and short-distance migrant species was higher in PAs than in NPAs, while occurrence of farmland species and LDMs was similar in all protection categories. PAs of Lombardy appear therefore effective only in protecting some categories of birds. Farmland and LDM birds would benefit more from ecologically sustainable land-use policies aiming at improving agro-ecosystem biodiversity than from protected areas.