Bio-based fertilizers (BBFs) are gaining attention as sustainable alternatives to mineral fertilizers due to their potential not only to enhance soil health and crop productivity, but also to close nutrient cycling. Derived from urban, agricultural or industrial origin, BBFs vary widely in composition, and their long-term impact on soil health and crop productivity remains insufficiently understood. To fill this gap, we evaluated the long-term effects (> 20 years) of various BBF applications, including compost, sewage sludge, cattle slurry and human urine on soil physical, chemical and biological properties, comparing them with conventional mineral NPK fertilizer in the CRUCIAL field experiment in Denmark. Our results showed that while mineral NPK fertilizers support crop productivity and improve certain soil properties, they do not deliver the broader soil health benefits associated with organic amendments. Indeed, compost and sewage sludge notably increased soil organic carbon (SOC), cation exchange capacity, soil porosity, water content at field capacity and microbial activity, while reducing bulk density and clay dispersibility. Human urine exhibited a comparable nitrogen fertilizer effect in terms of crop yields to the NPK treatment, highlighting its potential for urban nutrient recycling. Although values for human urine treatment did not exceed any critical thresholds, a higher sodium adsorption ratio than mineral NPK treatment and a negative trend for bulk density were observed, indicating a need for complementary organic matter input. Multifunctional soil health assessments confirmed superior performance of organic amendments (compost and sewage sludge) across chemical, physical, and biological indicators, primarily driven by sustained organic matter inputs. These findings underscore the positive effect of long-term application of BBFs - especially compost and sewage sludge – not only on SOC increment but also on soil physical, chemical and biological properties that are essential for sustainable crop production.
