Bioenergies are considered sustainable alternatives to fossil energy sources in the European Union (EU) renewable energy targets for 2030. However, their performances in terms of greenhouse gases (GHG) savings may be affected by indirect emissions related to the required land-use-change (LUC) that should be taken into account when modelling their sustainability. The European Renewable Energy Directive (RED) introduced a number of GHG emission criteria, in comparison with fossil fuels, that bioenergy deriving from agricultural biomasses must comply with. The Emilia-Romagna region (North-Eastern Italy), the second largest Italian biogas producer, has recently issued its Regional Energy Plan (REP), which set an ambitious increase of about 40% of the current installed electric power from biogas up to 2030. The aim of this study is to assess the sustainability of Emilia-Romagna REP accounting for the required indirect land-use-change (ILUC), due to the bioenergy crop expansion, potentially needed to reach the targets. Based on regional data available on biogas production, the amount of land used for maize silage to be destined to biogas production (as a model agricultural feedstock) has been calculated for the actual state-of-the art and towards 2030 scenarios provided by the REP. Starting from average GHG emissions associated with biogas production from 100% maize silage of 35 gCO2 eq/MJ, a further contribution of 8–18.5 gCO2 eq/MJ due to LUC has been found. Our findings indicate that it is difficult to assess the global GHG savings from the bioenergy targets fixed by regional energy plans when LUC effects are considered. Careful analysis is necessary in each case to avoid creating negative impacts.