Dental demineralization was determined in patients at three time points during fixed orthodontic treatment. A multiple cross-sectional study included 108 patients divided into three different groups: (1) beginning of orthodontic treatment; (2) one year into treatment; and (3) two years into treatment. Demineralization was estimated using a DIAGNOdent pen. We obtained data from multiple tooth-by-tooth demineralization readings combined with salivary pH and patients' oral hygienic and dietary behaviors. A t-test for independent samples and Spearman´s correlation were performed. No demineralizations differences were found between the initial stage and one year into treatment. Between one and two years small differences were observed, but demineralization increased between the initial stage and second treatment year, predominating in upper right central incisors (p = 0.056), upper left lateral incisors (p = 0.040), both upper canines (p = 0.055 and p = 0.040, respectively) and first left premolars (p = 0.034 and p = 0.053, respectively). We did not find associations between oral hygiene and dietary behaviours or salivary pH. In conclusion, demineralization occurred in first year of treatment and increased during second year, predominating in the upper arch and the left side mainly in upper right central incisors, upper left lateral incisors, both upper canines, and first left premolars.