Abstract <p>Understanding the population trends and seasonal fluctuations of the Indian flying fox, <i>Pteropus medius</i>, is crucial for developing effective conservation strategies. This study investigates these trends and fluctuations at eight permanent roosting sites within the semi-arid habitat of Kurukshetra district, Haryana, over two periods: April 2021–March 2022 and October 2022–March 2023. Significant monthly population fluctuations were observed, with peak colony sizes during the mating (September–November) and parturition periods (March–April), and the lowest populations during the peak summer months (May–July). There were significant differences (<i>P</i> ≤ 0.05) in mean population sizes between seasons and roosting sites. However, there were no significant differences (<i>P</i> ≥ 0.05) in mean population size between the two study years. Vijay Colony had the highest average population size, while Jyotisar had the lowest. Population fluctuations showed a negative correlation with ambient temperature (<i>r</i> = –0.113, <i>p</i> ≥ 0.05; <i>r</i> = –0.069, <i>p</i> ≥ 0.05) and precipitation (<i>r</i> = –0.117, <i>p</i> ≥ 0.05; <i>r</i> = –0.202, <i>p</i> ≤ 0.05), and a positive correlation with humidity (<i>r</i> = 0.123, <i>p</i> ≥ 0.05; <i>r</i> = 0.669, <i>p</i> ≤ 0.05). Additionally, the study identified significant threats to <i>P. medius</i>, including habitat destruction from tree cutting for commercial purposes, habitat disturbances from human activities, electrocution from power lines, and extreme summer heat. These findings highlight the urgent need for targeted conservation measures to mitigate these threats and protect the <i>P. medius</i> population in the study area.</p>