We investigated the association of outcomes with pre-pregnancy body mass index (ppBMI), Institute of Medicine (IOM) recommendations about gestational weight gain, and weight gain trajectories during pregnancy. A prospective cohort of 7866 pregnant women was recruited. ppBMI and weight gain at each follow up visit were collected. The outcomes were gestational diabetes mellitus (GDM), hypertensive disorders of pregnancy (HDP), caesarean delivery, macrosomia, small (SGA) and large (LGA) for gestational age, neonatal hypoglycemia. Group-based multi-trajectory modelling was used for weight kinetics during pregnancy. In the third trimester, 53.8% of women were above IOM recommendations, with an increased relative risk (RR) of HDP (1.91 (1.40–2.61)), caesarean (1.34 (1.15–1.56)), macrosomia (2.17 (1.77–2.67)), LGA (2.26 (1.83–2.80)), and hypoglycemia (1.89 (1.12–3.18)). Women with a weight gain above IOM recommendations in the second trimester who normalized their weight gain in third trimester had, compared to those who remained above IOM recommendations, fewer events of HDP (2.8% versus 5.3%, p = 0.008), caesarean delivery (16.9% versus 22%, p = 0.006), macrosomia (8.3% versus 14.2%, p < 0.001), and LGA (7% versus 13.2%, p < 0.001). Multi-trajectory modelling identified three profiles with continued variation in RR of complications, including GDM. Weight gain above IOM recommendations increased the risk of perinatal complications. A correction of excessive weight gain in the second trimester reduces these risks.