This study aimed to identify the prevalence of inadequate calcium and vitamin D dietary intake and related factors in two cohorts of pregnant women according to trimester of pregnancy. Two 24-hour dietary recall tests were taken in each trimester, one pertaining to weekends. Variables significantly correlated with intake of these nutrients were included in a multivariate linear regression model, adjusted for energy. Prevalence of inadequate intake was estimated according to the National Cancer Institute method (United States). In cohort A, inadequate vitamin D did not differ between trimesters; in B there was a reduction: from 99.7% in the first trimester to 97.1% in the third. In cohorts A and B, inadequate calcium intake exceeded 70%, falling slightly from the first (89.2% and 81.4%) to the second (79.7% and 69.1%) and third trimesters (82.7% and 72.6%). There was no correlation between maternal variables and the intake of these micronutrients. In conclusion, intake of vitamin D and calcium is seriously inadequate and distributed homogeneously among pregnant women in the primary healthcare network.