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The support of economic sectors that exploit natural bio-based resources in a particular region is an opportunity to benefit from local potentials in terms of sustainability, employment, output, and household income. Hence a relevant question emerges, namely, how can bioeconomy sectors be adequately supported? Within this context, another issue is whether the bioeconomy development strategy at a national level should be the same as that at a regional level. To address these issues, in the current study a comparison was made between the bioeconomy sectors at the country level based on the case study of Poland and one of the poorest regions in the European Union—the Lubelskie Region. A regional input–output model was built for the regional economy and compared with the national model. The bioeconomy-oriented regional input–output table was built by applying a hybrid regionalization method, combining non-survey techniques and a questionnaire survey that was carried out in companies of mixed bio-based sectors. Sectoral linkages, such as multipliers and elasticities, indicate notable differences among the bio-based sectors’ potentials of the regional and national economies. Therefore, a bioeconomy development strategy should be seen to differ at national and regional levels.