Background Women with polycystic ovary syndrome (PCOS) are at higher risk of developing pregnancy complications including gestational diabetes and preeclampsia. This study was performed with the aim of examining the impact of metformin on incidence of gestational diabetes and preeclampsia in pregnant women with PCOS. Materials and Methods: In this clinical trial, 88 pregnant women with PCOS with a history of taking metformin referring to Fatemieh hospital in Hamedan, Iran in 2017-18 were randomly assigned into two groups: metformin consumption (1000-2000 mg/day) continuing throughout the pregnancy and control (stopping metformin consumption immediately after detection of pregnancy). The pregnancy and fetal consequences and complications were compared in both groups. The data were analyzed by STATA software version 14.0. Results: In both groups, no significant difference was observed in terms of mean age, duration of infertility, body mass index, and baseline variables (p>0.05). The relative risk (RR) of incidence of gestational diabetes (RR: 1.97, 95% CI: 1.63 -2.39), preeclampsia (RR: 2.65, 95% CI: 1.95- 3.59), and abortion (RR: 2.33, 95% CI: 1.69 -3.22) was higher in the control group who did not continue metformin consumption throughout the pregnancy (p<0.05). The frequency of C-section was lower in the intervention group than in the control group (p<0.05). Conclusion: Based on the results of the present study, continuation of metformin consumption in women with PCOS during pregnancy may be associated with decreased adverse consequences of pregnancy including gestational diabetes and preeclampsia.