This work focuses on the assessment of the potential environmental benefits associated with the diversity of organic fertilisers available in the AGRIBALYSE database. Under the eco-design perspective, the shift from mineral to organic fertilisation regimes must not be over simplified, as fertilisation of each crop has an effect on the whole crop rotation. This work contrasts the environmental impacts of conventional crop rotations with equivalent eco-designed ones, featuring partial substitution of mineral by organic fertilisers at a level that the current yield is maintained. Two eco-design strategies involving AGRIBALYSE were devised. The first consists of retrofitting existing single crop processes by replacing conventional fertiliser inputs with newly available residual organic fertiliser processes. The second consists of eco-designing agricultural systems (i.e. technical itineraries representing crop rotations or crop sequences) by partially substituting mineral with newly available residues-based organic fertilisers. In both cases, it is necessary to adjust the fertiliser-related direct field emissions accordingly. In the second strategy, large amounts of organic fertilisers are input to replace mineral ones (tonnes vs. kg), and therefore overall impacts (i.e. impacts across impact categories) increase considerably, yet this effect is minimised when considering the alternative waste disposal pathways associated with the mineral fertilisation strategy (i.e. mineral fertilisation + disposal of the amount of organic residues necessary to deliver an equivalent level of fertilisation). The expanded functionality of a cropping system consuming organic waste-derived fertilisers (i.e. fertilisation + organic waste disposal) should be considered in comparative LCAs.