Purpose:Candida albicans is frequently detected together with Streptococcus mutans in the plaque or biofilms of children with early childhood caries (ECC). The aim of this study was to examine the association of the microbial counts of C. albicans and S. mutans in the supragingival plaque with the activity status of carious lesions and oral health practices in children with ECC. Materials and Methods: 66 children aged 5 years were examined and their caries status recorded as per the ICDAS-II and the Lesion Activity Assessment (LAA) criteria. A questionnaire covering oral health practices was administered to parents. Plaque samples were collected and cultured on mitis salivarus bacitracin (MSB) agar and CHROMagar. Data was analysed using Spearman's rank correlation and Mann-Whitney U test. Results: There was a statistically significant positive correlation between the levels of S. mutans and C. albicans (rs = 0.702, p <0.001). A positive correlation was seen between the percentage of active carious lesions with the colony counts of S. mutans (rs = 0.884, p <0.001) and C. albicans (rs = 0.785, p <0.001). Improper toothbrushing practices, dietary and feeding practices were statistically significantly associated with activity of caries lesions, S. mutans and C. albicans count. Conclusion: The total count of C. albicans and S. mutans in the supragingival dental plaque of children with ECC increases with an increase in the percentage of active carious lesions and the severity of dental caries. Improper oral health practices can lead to increased number of active carious lesions, as well as increased microbial load of both S. mutans and C. albicans.