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Packaging is lately identified as one of the biggest environmental problems and is at a focus of the scientific community and the industry aiming at minimizing environmental impacts. One of the most applied eco-design measures is to substitute traditional packaging materials with bio-based materials. One of the driving incentives for the packaging industry is the calculation of biogenic carbon (BC), even though there is no unified method for the calculation of credits from carbon sequestration. We developed a case study of paper-based packaging and tested the two variables important in the circular economy: (i) material, by modeling three different end-of-life scenarios; (ii) and time, by assessing the importance of this variable using bottom-up and top-down calculations. The results of the case study showed that credits from carbon sequestration could lead to undesirable linear pathways of the EoL, by giving the biggest credits for landfilling and, thus, contradicting the circularity principles. Moreover, the time variable is critical for the calculation of biogenic carbon. Credits for carbon sequestration for short-lived products can lead to an overestimation of the storing impact because the top-down calculus of national inventories, developed based on the UNFCCC method, cannot register carbon savings. This short communication indicates that we need to invest in additional research to identify the correct way to calculate the carbon credits when using bio-based materials and to improve the practice for calculations of the overall carbon footprint of the short-lived materials in the technosphere.