Organic fertilizers are important in agroecosystems, but the fate of specific forms of added phosphorus (P) in the long-term is not well understood. We studied the effects of 62 years of application of three organic fertilizers (dairy manure, compost and dried sewage sludge) on organic P forms in the topsoil as characterized by solution 31P NMR spectroscopy and enzyme additions in a field experiment on a slightly acidic Luvisol in Switzerland. Changes in inorganic P extracted with NaOH–EDTA were related to the P-input–output balances of the treatments, which ranged between − 13 kg P ha− 1 yr− 1 in the non-fertilized control and + 93 kg P ha− 1 yr− 1 with sewage sludge application. The majority of extractable P in the applied organic fertilizers (68–91%) was in the form of orthophosphate. The fertilizers differed with respect to specific organic P compounds identified by 31P NMR, with myo-inositol hexakisphosphate (myo-IP6) found in compost and dried sewage sludge, but absent from dairy manure. A small amount of scyllo-inositol hexakisphosphate (scyllo-IP6) was additionally found in compost. However, the specific forms of organic P in topsoil extracts remained unaffected, with similar concentrations of myo-IP6, scyllo-IP6, pyrophosphate and degradation products of phospholipids and nucleic acids present in all treatments. Using enzyme additions, a significant accumulation of non-hydrolyzed P in soil amended with dried sewage sludge was observed, but it accounted for only 9% of the total accumulation of P in this treatment compared to the treatment with manure addition which had an even input–output P balance. The similar composition of organic P in all treatments suggests that specific organic P compounds added with the three organic fertilizers were completely transformed in the topsoil or lost from it.