Jerusalem artichoke (Helianthus tuberosus L.) is a plant with considerable potential for energy generation due to its rapid growth, high biomass yield, and resistance to environmental stresses. The aim of this study was to determine the influence of the nitrogen fertilization strategy on the yield and energy balance in the production technology of Jerusalem artichoke (JA) in a perennial cropping system. The article presents the results of a three-year experiment which was conducted in Poland to determine the effect of different N rates (0, 50, 75, and 100 kg ha−1) supplied with mineral fertilizers and liquid digestate on the energy balance in the production of JA aerial biomass. The experiment had a randomized block design with three replications. The demand for energy in JA cultivation reached 16.2–26.3 (year 1) and 2.9–14.6 GJ ha−1 (years 2 and 3). Energy inputs in the cultivation technology were reduced by 17–19% (year 1) and 35–47% (years 2 and 3) when mineral fertilizers were replaced with digestate. Jerusalem artichoke yields were lowest in the technology without fertilization (12.5 Mg ha−1 DM). Dry matter yield increased significantly (by 43–55%) after the application of 75 kg N ha−1, regardless of fertilizer type. The energy output of biomass peaked (230.1 GJ ha−1) in response to a mineral fertilizer rate of 75 kg N ha−1. In turn, the highest energy gain (218.5 GJ ha−1) was noted after the application of digestate at a rate equivalent to 75 kg N ha–1. The energy efficiency ratio was highest in the technology without fertilization (20.1) and after the application of digestate at a rate equivalent to 75 kg N ha−1 (19.7). Regardless of the factors that limit agricultural production, the energy balance of JA biomass production was most favorable when JA was fertilized with digestate at a rate equivalent to 75 kg N ha−1. The results of this study may pave the way for future research on novel agronomic strategies for sustainable bioenergy production, including nutrient recycling.