Spreading of pruning waste over the soil surface may increase soil organic carbon, thus improving soil physical properties and serving as a source of nutrients and energy for microbial populations. The aim of this study was to test the effect of the environmental conditions and the biochemical composition of pruning waste from avocado, cherimoya, mango and gardens on their decomposition process in a Mediterranean subtropical climate. Bagged pruning and garden waste were placed on the ground at a distance of 1 m around the trunk of the three trees from each crop. The concentrations in C, N, lignin, cellulose, hemicellulose, other extracts and ash were determined at the beginning of the experiment (T0), after six (T6) and 24 (T24) months in the field. Initially, significant differences were detected for all types of waste, especially in lignin, hemicellulose, cellulose and other extracts. No significant differences were found in the N content and the C content in mango pruning waste was significantly lower than that in avocado. The greatest weight loss recorded at T24 (63.2%) was related to the lower content in lignin, cellulose and other extracts. Weight losses and C concentrations showed negative correlations with lignin content. Despite the intense decomposition of all the waste, between 55 and 36.8% of the original weights were recorded at the end of the experiment. Recalcitrant C could be the result of the lignin concentrating in the case of the garden waste applied to the different crops.