Organic wastes contain significant amounts of organic matter and nutrients and their recycling into agriculture can potentially contribute to closing the natural ecological cycle. The aim of this study was to evaluate the improvement in overall soil fertility and soil nitrogen (N) supply capacity in a long-term field experiment with repeated application of different urban and agricultural organic waste amendments. Soils from the CRUCIAL field experiment in Denmark, in which diverse types of urban (human urine, sewage sludge, composted household waste) and agricultural wastes (cattle slurry, farmyard manure and deep litter) have been applied annually for 11 years (at normal and accelerated rates), were used to estimate the effects of the different qualities of organic wastes on soil fertility, N turnover and crop N availability. Soil physical fertility parameters, such as water retention and total carbon, improved with the application of organic wastes. Cattle manure, sewage sludge and composted household waste in single or accelerated rates of application increased soil total N by 13–131% compared to the mineral fertiliser NPK treatment. The highest net N mineralisation capacity was observed for the accelerated rate of composted household waste, followed by all the other organic waste amendments and with the lowest net N mineralisation in the NPK-only and the unfertilised treatments. In soils amended for 11 years with NPK, human urine, cattle slurry, sewage sludge, cattle farmyard manure, cattle deep litter and composted household waste, the apparent crop N-use efficiencies (NUE, compared to unfertilised control) were 88, 73, 55, 51, 21, 16 and 11%, respectively. The continuous application of organic wastes generally increased NUE in the last year in comparison with the first year, except for composted household waste where N-use efficiency declined from 27 to 11%. The corresponding long-term mineral fertiliser N-equivalent (MFE) value ranged between 82% (human urine) and 13% (compost). Overall, continuous application of organic wastes improved soil fertility, with low C:N waste improving soil N availability, crop uptake and NUE the most, while the most C-rich and high C:N organic wastes (cattle deep litter and household waste compost) had a negative effect on crop NUE over time.