Dietary changes during pregnancy (DP) and post-partum are essential for women’s nutrition status and the health of their offspring. We compared the diet quality DP and at 3-year postpartum (3YPP) and assessed the relationship between maternal diet quality and nutritional status using a prospective cohort design among women in East Jakarta. In total, 107 women were recruited from the study in 2014 and followed up at 3YPP in 2018. The mid-upper arm circumference (MUAC), weight, and height were evaluated. Food consumption data were collected from repeated 24-h recalls. The validated US Diet Quality Index-Pregnancy (DQI-P) scores with eight components were calculated using the food consumption data and compared between DP and 3YPP. Associations of the DQI-P score with the MUAC and weight gain DP and body mass index (BMI) at 3YPP were analyzed using multivariable linear and logistic regression. The median of the DQI-P score DP was significantly higher than at 3YPP [35 (27; 42) versus 27 (19; 30); p-value <0.001, respectively]. The higher DQI-P score was associated with increased weight gain DP of 3.3 kg (adjusted β = 3.30, 95% confidence interval = 1.06–5.54) after adjusting for the mother’s age and household income. The DQI-P score was not associated with an increased risk of chronic energy deficiency DP and overweight–obesity at 3YPP. Thus, the diet adequacy was associated with weight gain DP but did not affect the MUAC DP and BMI at 3YPP. The DQI-P score DP was slightly better than the diet at 3YPP; however, the overall diet quality was inadequate. In conclusion, a higher DQI-P score was associated with increased weight gain DP of 3.3 kg but was not associated with other nutritional status indices in DP and 3YPP. Innovative dietary quality improvement programs are required to reduce malnutrition risk in pregnant and reproductive-age women.