The study was focused on the assessment of cup-plant (Silphium perfoliatum L.) as a potential feedstock for biogas production in comparison to reference maize related to the balance needs of nutrients and some microelements for their cultivation, especially with use of digestate for fertilization. Field experiments were carried out in areas of the Czech Republic with less favorable conditions for the cultivation of maize. Obtained results confirmed that cup-plant can be considered a promising novel crop for biogas production due to high yields of biomass (12-18 t/ha DM) and methane (3600-4250 Nm3/ha) competing with reference maize grown under the same soil and climatic conditions. The biochemical analyses characterizing the feed value of phytomass were conclusively better with maize than cup-plant. This corresponds with specific methane yields, which is about 5-10% higher in maize (269-319 Nm3/t VS) than in cup-plant (254-298 Nm3/t VS). On the basis of chemical analyses of tested crops, the uptake of basic nutrients (N, P, K, Ca, Mg and S) and selected trace elements (microelements B, Fe, Mn, Co, Cu, Mo, Ni and Zn) was determined. Then, using the element contents and average yields, it was possible to calculate the annual removal of each element from the field with cup-plant and reference maize as the basis value for the evaluation of compensatory fertilization needs. With respect to the cultivation of tested crops for biogas production, the possibilities of their compensatory fertilization were evaluated using digestate from biogas plants. The uptake of different nutrients and microelements on tested crops was verified. The experiment showed that cup-plant has higher requirements on all tested nutrients, except N, and microelements, except Cu and Zn. In the case of nutrients, the highest uptake differences between cup-plant and maize were at B (about 11× higher), followed by Mg (3.5×) and K (1.8×). In the case of microelements, the highest uptake differences were B at (about 9× higher), followed by Co (5×), Fe, and Mn (2×). Therefore, increasing yields of cup-plant after using these nutrients and microelements for compensative fertilizing can be expected. For the mixture of maize and cup-plant (1:1 of VS weight), the higher specific methane yield was obtained (292 Nm3/t VS). It was more than expected of the average value (286 Nm3/t VS). It cannot be explained by the improvement in the feed value of cup-plant and maize mixture, but a possible explanation could be the positive synergistic effect of cup-plant due to the better supply with biologically active essential nutrients and microelements. In any case, this phenomenon deserves more detailed research in the future.