Bio-fertilizers could be a possible solution to help manage bio-waste problems and to maintain soil health conditions, especially in organic farms. Pruning of cactus pear produces from 6 to 10 tons/yearly of cladodes per hectare in specialized Italian orchards, which represents waste and a cost for disposal to farmers. Therefore, the aim of the work was to investigate the effects on soil physical properties, microflora activity, and basil plant growth of powdered pruning waste from cactus pear incorporated in the soil (10%, 20%, 30% 40% w/w). Moreover, we studied a dynamic composting process from fresh cladodes to produce stabilized end-products at the farm level. Our studies demonstrated that holding water ability and bulk density of soil were ameliorated by supplementing dried cladodes. Thus, gravitational and gravimetric water was positively correlated with the increase of added dried cladode in the soil (0.1% and 6.2 g H2O ± 0.3 in samples of 40% mixed soil versus 68% and 3.3 g H2O ± 0.3 in control). Furthermore, bulk density was reduced limiting soil compaction. Preliminary results on microbial activity suggested a possible selection/inhibition of some bacterial strains correlated with the increment of dry cladode supplementation. The basil plants grown in 20% mixed soil showed an increased biomass when compared to the control (+ 21%). Finally, raw cladode proved to be an excellent substrate for aerobic fermentation providing a final product of good quality and high moisture content (65%). These results are particularly relevant in organic agriculture where bio-fertilizers are recommended as economical, eco-friendly solution accessible also to marginal and small farms.