INTRODUCTION: Few studies have described subgingival microbiota in pregnant women with mild preeclampsia. OBJECTIVE: Clinical periodontal and subgingival microbiota changes were identified in pregnant women with mild preeclampsia after periodontal treatment. MATERIALS AND METHODS: In a secondary analysis of a randomized clinical trial, 57 preeclamptic women were studied at Hospital Universitario del Valle in Cali, Colombia. Thirty one women were randomized to the periodontal intervention group (subgingival scaling and planing ultrasonic and manual) during pregnancy and 26 to the control group (supragingival prophylaxis). Periodontal clinical parameters and subgingival microbiota were characterized at the time of acceptance into the study and again at postpartum. Eight periodontopathic bacteria and 2 herpesviruses were assessed by polymerase chain reaction. Chi-square, McNemar or Student's t tests were used, with a significance level of p≤0.05. RESULTS: Both groups were comparable in the clinical and microbiological variables at baseline. Periodontal treatment reduced the average pocket depth in the intervention group from 2.4±0.3 to 2.3±0.2 mm (p<0.001) and in control group 2.6±0.4 to 2.44±0.4 mm, (p<0.001) and bleeding index 16.4±1.5% to 7.9±0.7% in the intervention group(p<0.001) and 17.1±1.8% to 10±0.9% in the control group (p=0.002). The frequency of detection of microorganisms did not differ significantly between groups. CONCLUSION: Scaling/root planning and supragingival prophylaxis significantly reduced the probing depth and gingival bleeding index. Periodontal treatment was not more effective than prophylaxis in reducing periodontopathic organisms or herpesvirus