Desensitization (DSZ) or oral tolerance induction is increasingly used in children who do not outgrow their food allergies. Off-label omalizumab (OMZ) is used as adjuvant therapy for those with severe reactions, but there is little information on outcomes when OMZ is withdrawn. The long-term outcome in a group of children with severe milk or egg allergy who had undergone an OMZ-assisted DSZ procedure is here described. Clinical data from 21 children from the time they started DSZ until database closure were retrospectively collected, to assess the appearance of symptoms and response to clinical decisions under real-life conditions. Patients received OMZ before, during, and after the DSZ procedure itself and OMZ was subsequently discontinued. The scheduled treatment protocol had to be changed in almost all patients due to reactions or individual needs. Three of 21 patients had to prematurely abandon the procedure due to DSZ failure. The other 18 patients were able to tolerate the target dose of food, but nine of them developed symptoms when eating the food 1.5 to 6 months after stopping OMZ. These patients underwent a second course of OMZ-assisted DSZ, which was successful in six, but three had a second relapse 3 to 8 months after stopping OMZ and decided to quit. OMZ-assisted DSZ failed in almost a third of patients with severe allergy even after a second course of OMZ, almost 40% had a successful outcome with one course of OMZ, while almost a third required a second course. Relapses of symptoms occurred up to six months after stopping OMZ.