Soil nutrient imbalance is a global threat to food security and ecosystem sustainability but adding organic residues or constructing anthropogenic soils and technosols can optimize it. However, FAO considers organic residues not “risk-free”, mainly due to their heavy metal content. Despite the fact that applying pruning residues to soil is a worldwide fertilization practice, its potential heavy metal risk has been poorly studied. This work characterizes Cu, Zn, Cd, Cr, Ni and Pb elemental composition concentration and their solubility content in almond tree pruning, commercial peat substrate, hay straw, olive tree pruning, pomegranate peel, pine needle, date palm leaf pruning, sewage sludge compost and vine pruning. Furthermore, we compare the legal frameworks governing heavy metal content in agricultural substrates to heavy metal concentration in each residue. Results show that commercial peat substrate is the only one among those studied that surpasses the threshold value for Cr in agricultural substrates. All pruning residues met the heavy metal threshold value; hence, their application to soil involves minimal soil toxicity. Moreover, the solubility index of heavy metals and the maximum quantity of each residue are crucial to discerning a heavy metal-free organic fertilization plan.