Background: Anupreksha-based meditations (AM) involve focusing on objects including images, colors, sounds, and the nature of the body and soul. Similar to Preksha meditation, which has shown positive effects on mental and physical well-being, AM is proposed to have potential benefits. However, the impact of AM on negative thinking, a key factor in various psycho-physiological ailments, has not been thoroughly examined. This study aimed to explore the effectiveness of AM in reducing negative thoughts and improving mental-health and well-being. It hypothesized that practicing AM can positively alter thought patterns and enhance overall well-being. Methods: A total of 462 English-speaking participants aged 19 to 60 years. Among them, 233 were regular AM practitioners with at least 12 months of experience, and 229 were non-meditators. Self-reported scales were used to measure perseverative thinking, mindfulness, self-compassion, and spiritual well-being. Results: Data were checked for normality and the Mann-Whitney U-test was performed. The AM group showed significant lower perseverative thinking scores (p<0.001) and higher mindfulness, self-compassion, and spiritual well-being scores (p<0.001). The scores of perseverative thinking negatively correlated with mindfulness (rho -0.53; p<0.001), self-compassion (rho -0.43; p<0.001), and spiritual well-being (rho -0.22; p<0.001) in meditators. Additionally, mindfulness positively correlated with self-compassion (rho 0.42; p<0.001) and spiritual well-being (rho 0.36; p<0.001). Conclusions: Shreds of evidence indicated that the practice of Anupreksha-based meditations alleviates negative thoughts by promoting mindfulness, self-compassion, and spiritual well-being. Therefore, the AM can be suggested to improve the positive state of mind and also can be practiced to mitigate psychological-related issues.