What are the effects, measured as flows of biogenic carbon, plant nutrients, and pollutants, of moving organic waste up the waste hierarchy? We present a case study of Denmark, where most of the organic fraction of household waste (OFHW) is incinerated, with ongoing efforts to increase bio-waste recycling. In this study, one-third of the OFHW produced in North Zealand, Denmark, is diverted away from incineration, according to the Danish Waste Resource Plan 2013–2018. Co-digestion of OFHW, and digestate application on agricultural soil, utilizes biogenic carbon, first for energy conversion, and the remainder for long-term soil sequestration, with additional benefits for plant nutrient composition by increasing the N:P ratio in the digestate. We show a dynamic model of the biogenic carbon flows in a mix of OFHW co-digested with livestock manure and sewage sludge, addressing the contribution of OFHW to long-term carbon sequestration compared to other agricultural residues and bio-wastes over a time span of 100 years. In addition, we trace the associated annual nutrient and cadmium loads to the topsoil. At constant annual input rates and management practices, a diversion of 33% of OFHW would result in an increased organic carbon build-up of approximately 4% over the current amounts applied. The addition of OFHW, moreover, beneficially adjusts the N:P ratio of the digestate mix upwards, albeit without reaching an ideally high ratio by that measure alone. Cd loads from OFHW remain well below regulatory limits.