In Europe, the estimation of Lyme borreliosis (LB) incidence is challenged by its heterogeneous reporting. In France, LB incidence is estimated from cases reported voluntarily to the Sentinelles network through general practitioners (GPs). Here, we explored how a computerised decision support system (CDSS), Antibioclic, with higher GPs participation and country-wide coverage, can inform further LB incidence. We derived the incidence of LB Antibioclic indicators (with either erythema migrans or disseminated disease), surveyed Antibioclic usage for suspect cases seen in GP consultations, and compared those estimates with the Sentinelles network estimations. In 2023, the incidence of Antibioclic LB indicators (290 per 100,000 inhabitants; CI95%, 277-303) was almost five times higher than LB incidence from the Sentinelles network, but sharing similar higher-incidence regions. Antibioclic LB indicators under-estimated the incidence of suspect cases seen in higher-incidence regions, while in lower-risk regions, Antibioclic estimation was closer to observed suspect cases. Refine estimates would benefit from improved follow up over time and space while improving case definition.