(1) Measuring usual iodine intake is a complex task due to the food consumption variability and its natural concentration in food. Therefore, the use of covariates to adjust statistical methods to estimate usual intake could improve the estimates obtained through dietary surveys. This study aims to evaluate the influence of salt and seasoning usage covariates on the estimates of usual iodine intake and the prevalence of its inadequacy. (2) A cross-sectional study was conducted with Brazilian pregnant women’s food consumption data obtained with 24-h recall (n = 2247). The usual iodine intake was adjusted for intraindividual variability, supplement use, temporal effects, data collection methods, and sociodemographic characteristics with the tool UCD/NCI SIMPLE in the SAS software. Then, salt and seasoning usage covariates were used to adjust the distribution. The harmonized intake reference values for populations were used to assess intake adequacy. (3) The adjustments for salt and seasoning usage yielded a higher mean of usual iodine intakes. The only exception was the adjustment for the “habit of adding salt to meals after preparing/cooking”, which produced a lower mean of usual intake and increased the prevalence of insufficient intake. (4) Salt and seasoning usage covariates affect the estimates evaluated. However, more studies are necessary to evaluate the influence observed.