The risk of developing white spot lesions (WSLs) after orthodontic treatment with lingual brackets is generally considered lower than with labial ones, even if plaque accumulation is frequently higher due to the increased difficulty level in oral hygiene maintenance. In this prospective clinical study, selective enamel etching technique effectiveness in reducing plaque accumulation and WSLs was tested. Thirty patients were bonded with a split-mouth approach: two randomly selected opposite quadrants were used as the test sides, using customized plastic etching guides, and the other two as control sides, applying traditional direct etching methods. The plaque presence around the braces was recorded after 1, 3, 6, and 12 months according to a lingual plaque accumulation index (LPAI), as was the presence of WSLs. PAI measured values were significantly higher in the control sides during the observation period. Test and control sides differed significantly for new WSL onset only after 12 months of treatment. Therefore, the present research demonstrated that this guided enamel etching technique allowed for significant reduction in plaque accumulation around the lingual brackets and reduced onset of white spots after one year of treatment.