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. Codigestion 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.