Background Poor diet is a risk factor for anemia, overweight, and obesity among adolescent girls. However, comprehensive assessment on dietary quality and habits in this population is limited. We assessed the association of meal patterning, dietary quality, and dietary diversity with both anemia and overweight-obesity. Methods We conducted a cross-sectional survey in 335 school-going adolescent girls aged 12-19 years from three districts in West Java using multi-stage cluster sampling. Meal patterning, Dietary Quality Index for Adolescents (DQI-A), and Dietary Diversity Score (DDS) were determined using 2-day 24-h recall. Results Of the girls, 45% were anemic and 17% overweight or obese. Eating occasions of 3-4 times (AOR 2.68, 95% CI 1.21-5.98) and >4 times (AOR 2.43, 95% CI 1.01-5.83) were associated with greater odds of developing anemia compared to eating occasions of <3 times. Adolescent girls who skipped dinner had greater odds of being overweight or obese (AOR 2.13, 95% CI 1.10-4.10) and were less likely to be anemic (AOR 0.56, 95%CI 0.33-0.95) compared to those who did not skip dinner. Difference in energy intake was found between girls who had dinner and skipped dinner (p = 0.05). Mean total DQI-A score was 44.4% ± 7.71% and DDS was 4.0 out of 9.0. DQI-A score was significantly higher in non-anemic compared to anemic girls. Moreover, each unit increment of 1% of total DQI-A score was associated with a 3.967 g/dL increases of hemoglobin after adjustment for confounders. We found differences in total DQI-A score between normal-weight and overweight or obese girls. DDS score was not significantly different between groups, although lower meat, chicken, and fish consumption were correlated with anemia (p<0.01). Conclusions Overall, the girls had poor dietary quality and diversity. The findings therefore indicated the importance of improving dietary quality and diversity in a regular meal pattern, especially meal frequency and meal skipping, to reduce the risk of anemia and overweight-obesity among adolescent girls.