It has previously been established that the sp3/sp2 ratio influences the type of degradation (direct or indirect) as well as the production of oxidants at boron-doped diamond (BDD) films. However, there are no published studies on the effects achieved (in terms of degradation performance) when an ionic liquid is treated nor any evaluations of effluent toxicity after treatment. For this reason, this study investigated the influence of the sp3/sp2 ratio of BDD anodes on the degradation of the ionic liquid 1-butyl-3-methylimidazolium chloride. The presence of a large fraction of C-sp3 favored more efficient mineralization (significant at high current densities); however, phytotoxic analyses revealed a more toxic final effluent. Depending on the experimental conditions and the sp3/sp2 ratio, smaller amounts of undesirable chlorate and perchlorate anions as well as different oxidation by-products were detected, consequently affecting the toxicity level of the effluent. The results are discussed and compared with the existing literature.