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Simple Summary: This study addresses the critical issue of disease resistance in Apis cerana indica colonies by focusing on their hygienic behavior and other key characteristics essential for colony health. By evaluating colonies across different seasons and locations in Tamil Nadu, India, this research aims to identify colonies with superior hygienic behavior and overall performance. Through comprehensive field analysis and statistical methods, this study reveals subtle variations, emphasizing the importance of seasonality and location-specific factors. The findings provide valuable insights into the distribution of hive metrics and the relationships between hygienic behavior and other colony parameters. This knowledge will aid in the selection of robust colonies to combat prevailing diseases and pests, enhancing the sustainability and productivity of A. cerana indica beekeeping. Hygienic behavior (HB) emerges as a pivotal trait, impacting colony resistance to diseases. This study aimed to understand the behavioral traits of Apis cerana indica colonies, with a focus on HB and other key characteristics crucial for colony health, and to screen and identify colonies with superior hygienic behavior and better performance to combat prevailing diseases and pests. This research spans a comprehensive field analysis with different seasons and locations, encompassing the distinct environmental and management factors that influence honey bee behavior. The inclusion of A. cerana indica colonies from various locations provides a novel perspective, offering valuable insights regarding the hygienic behavior of A. cerana indica. Several statistical analyses, including descriptive statistics, principal component analysis (PCA), and Aligned Rank Transformation-Analysis of Variance (ART-ANOVA) for repeated measures, shed light on the distribution of hive metrics, emphasizing the significance of considering seasonality and location-specific factors. PCA highlights unique characteristics in Tirupur and Coimbatore colonies, while correlation analyses uncover relationships among HB, honey, pollen, brood area, and adult population. Moreover, the study's nuanced findings gave the status of hygienic behavior of A. cerana indica colonies and identified colonies with better colony performance, which will be useful for future breeding programs with A. cerana indica. [ABSTRACT FROM AUTHOR]