Greenhouse Gas (GHG) emissions is a topic of major concern worldwide. Following previous articles which provide a methodology for estimating GHG emissions associated with international trade by transport mode at the world level, in this paper, we estimate an equivalent database of GHG emissions for inter-regional trade flows within a country (Spain). To this end, we built a new database of GHG emissions for origin-destination flows between Spanish provinces during 1995-2015. For each year, we combine industry-specific flows by four transport modes (road, train, ship and aircraft) with the corresponding GHG emissions factor for each mode in tons*km, drawn from the specialized literature. With this dataset of GHG emissions, we generate and analyze the temporal, sectoral and spatial pattern of Spanish inter-regional GHG flows. We then forecast emissions for 2016-2030 and consider how transport mode shifts might produce a more sustainable freight system within the country through the substitution of environmentally friendly alternatives (railway) for specific origin-destination-product flows in high-polluting modes (road).