This article examined the opportunities and challenges of mapping emissions associated with value chains in a subregional context, using the Basque Country as a case study. By leveraging symmetric input–output tables, the study reconstructed industrial value chains and quantified their related emissions to assess sustainability implications. The methodological approach revealed both the potential and limitations of conducting such analyses at a subregional level, highlighting key methodological and data constraints. The findings contribute to a more precise understanding of the carbon footprint of firms operating in the region and offer insights into the data availability required for similar assessments. Moreover, the methodology employed makes it possible to reveal the emissions embedded in imports, as well as the locally generated emissions embedded in exports—an issue that becomes particularly relevant in the case of subregional entities. This study also applied a novel input–output analysis method for deriving value chains, enhancing the methodological framework for emissions mapping in regional contexts.