Abstract Background Maternal smoking during pregnancy represents a significant risk, increasing the adverse consequences for mothers and newborns. Different national targets have been developed in Germany to reduce smoking rates during pregnancy. To monitor the achievement of these goals, this study aims to assess social differences and temporal trends of smoking behaviour during pregnancy in mothers living in Germany. Methods Data of children aged 0 to 6 with valid information on maternal smoking habits during pregnancy were subtracted from German Health Interview and Examination Survey for Children and Adolescents (KiGGS)(KiGGS baseline 2003-2006, n = 6,525 and KiGGS wave 2 2014-2017, n = 4,838). The information on maternal smoking during pregnancy was recorded retrospectively as part of a self-administered written questionnaire. We estimated the prevalence of smoking in pregnancy and multivariable logistic regression models to assess the association with the age of the mother at the time the child was born, the socioeconomic status of the family and the migration background. In addition, to analyse trends over time, we compare the current data with the KiGGS baseline study. Results The prevalence of mothers who smoked during pregnancy decreased statistically significant from 19.9% (KiGGS baseline) to 10.9% (KiGGS wave 2). Younger mothers aged up to 24 years were more likely to smoke during pregnancy (OR 1.74; 95%CI 1.04-2.89), similar to those with intermediate (OR 5.52; 95%CI 2.90-10.48) or low socioeconomic status (OR 22.43; 95%CI 10.84-46.39), and those without (OR 4.18; 95%CI 2.27-7.70) or with one-sided migration background (OR 2.47; 95%CI 1.26-4.84), in comparison to the groups of reference. Conclusions Our findings, present the reduction of smoking prevalence during pregnancy, recognising the effectiveness of the tobacco control programs in Germany. However, more emphasis on the prevention strategies for young and socially disadvantaged women are still required. Key messages Smoking prevalence during pregnancy has decreased in Germany over time, though still represents a challenge for public health and tobacco control. The prevention strategies should reduce the social breach, to extend the benefit among women and their offspring.