Dragon fruit is a prominent substance in global agriculture. Despite this, it is gaining popularity and is a viable solution in resource-poor, environmentally degraded areas because of its many health benefits. Nevertheless, many dragon fruit plantations have been impacted by the disease, reducing their yield, and the detection system is still conventional. Farmers’ lack of disease identification and management expertise diminished crop quality and products. As a result, little research was carried out to assist those specific farmers requiring adequate agricultural support. This research has proposed an autonomous agro-based system to recognize dragon diseases using in-depth analysis of feature selection techniques. After the collection of real-time images of the dragon, the images are preprocessed using various image-processing techniques. The two important features are retrieved after segmentation. The analysis of variance (ANOVA) and the least absolute shrinkage and selection operator (LASSO) are used as feature selection techniques to assess the feature rank based on the mutual score. To analyze the effectiveness of the machine learning algorithms that were used, six distinct machine learning classifiers were applied to the top-ranked feature sets, and their performance was measured using seven distinct performance evaluation metrics. AdaBoost and Random Forest classifiers for the LASSO feature ranking approach got the maximum accuracy, which is 96.29%, based on a comparison of classifiers based on the ANOVA and LASSO feature set. Despite this, we have optimized the computational resources of each classifier for the LASSO feature set.