Soil fertility management in organic systems, regulated by the organic standards, should seek to build healthy, fertile soils and reduce reliance on external inputs. The use of nutrients from conventional sources, such as animal manures from conventional farms, is currently permitted, with restrictions, in the organic regulations. However, the reliance of organic agriculture on the conventional system is considered problematic. In light of this, the organic sector in Denmark has recently decided to gradually phase out, and ultimately ban, the use of conventional manures and straws in organic agriculture in Denmark. Core focal areas for phasing out conventional nutrients are as follows: (1) amendments to crop selection and rotations, (2) alternative nutrient sources (organic wastes) and (3) increased cooperation between organic livestock and arable farmers. Using Denmark as a case, this article discusses the background and implications of the strategy to phase out conventional manure and straw, and explores possible solutions to the challenge of ensuring a sustainable nutrient supply to organic systems. Alternative strategies to ensure nutrient supply will require a tapestry of small solutions. One element of this tapestry is to review the volume and type of nutrient sources available in alternative, non-farm organic waste streams and consider their suitability for use in organic systems.