Neurexins are key synaptic cell adhesion molecules involved in synapse specification and maturation. They couple synaptic activity and cell adhesion to regulate activity-dependent synapse development. Recently, neurexin processing by alpha- and gamma- secretases has been reported. In the present study, we characterized the sites at which Nrxn3beta is processed by alpha- and gamma- secretases, identified the enzymes responsible for the shedding, characterised the fragments resulting from the cleavage and investigated the potential functions of generated fragments. We show that Nrxn3beta is shed at two sites- one processed by ADAM17, the other by ADAM10. The shedding generates two soluble ectodomain (sNrxn3beta) fragments and two C-terminal fragments (CTFs). Each CTF is further processed by gamma-secretase to generate one intracellular domain (ICD) and multiple P3-like or Abeta-like fragments. We show that the production of the main sNrxn3beta generated by ADAM10 affects axonal bouton development and spinogenesis during adult newborn neuron development in vivo. Moreover, we demonstrate that sNrxn3beta affects the expression of genes associated with regulation of synaptic vesicle exocytosis (Rab3a), NMDA receptor subunit composition (Grin2c) and metalloprotease inhibition (TIMP-1). Furthermore, we report first evidence that the ICD generation might influence the levels of a protein responsible for the NMDA delivery to dendritic sites (KIF17). The investigation of properties of neurexin P3-like and Abeta-like fragments revealed a tendency of Abeta-like fragments to form oligomers and exert a toxic effect in primary cortical neurons. Our study shed light on the molecular pathways regulated by neurexin cleavage fragments and their possible implications in different pathologies.