Recently, on the EU market, phosphonic acid residues were detected in many organic goods, although fosetyl-derivates and phosphite salts are not allowed by Reg. EC n. 889/2009. The BIOFOSF project “Solving phosphite issue in organic fruit and horticultural crops” aimed at verifying whether the phosphonic acid contamination could be due to unproper use of fertilizers/plant protection products by organic farmers, or to the plant’s ability to self-produce it spontaneously. Applying a participative approach, field case-studies on potato, rocket lettuce, and pears were carried out (organic vs. integrated systems). The ethyl-phosphonic acid and phosphonic acid were determined in soil, tubers, leaves, fruits, tree woody organs, used fertilizers, and plant protection products to correlate them to the applied farming management. Tested crops were not able to self-synthetize phosphonic acid, being its detection due to: (i) external inputs not allowed in organic farming; (ii) fertilizers/plant protection products allowed in organic farming, contaminated by fosetyl or phosphite. In addition, it was found that tree crops can stock the phosphite in their woody organs, then translocate it from branches to leaves and fruits over time. Regression models applied to field data showed that fruit trees decontamination could take more than 5 years, depending on the starting value of phosphonic acid contamination, useful to define the phosphite maximum residue limit in organic fruit crops.