Nutrient deficiency in vegetables is a significant challenge for meeting the dietary needs of a growing population and improving the nutritional quality of bottle gourd (Lagenaria siceraria L.) through organic inputs can address this issue. An experiment was conducted at the Department of Vegetable Science, Tamil Nadu Agricultural University (2023-2024) aimed to enhance the nutritional quality of bottle gourd through organic methods. The research was conducted using a Randomized Block Design (RBD) with 11 treatment combinations and control, the study focused on improving its nutrient content, avoiding pesticide residues and supporting eco-friendly cultivation. Statistical analyses such as ANOVA, Principal Component Analysis (PCA), path analysis, phenotypic correlation and heat map analysis were used to evaluate the effects of organic inputs on the nutritional quality and market value of bottle gourd, ensuring better health benefits. Results from Season I and Season II revealed that treatment T-9, which incorporated (Farmyard manure, Vermicompost, Neem cake, 3G extract, five-leaf extract, Panchagavya, Fish fermented extract, Egg fermented extract, Bacillussubstilis), treatment T-9 yielded the highest nutritional quality in bottle gourd, including protein (0.0275%), ascorbic acid (8.61%) and total ash (6.27%). It also had the highest macro and micronutrient levels, such as phosphorus (19.1 mg/g), potassium (1.74 mg/g), calcium (30.2 mg/g), copper (0.066 mg/g), iron (0.038 mg/g) and selenium (0.318 mg/g), showcasing its superior nutritional profile. These findings suggest that organic inputs, particularly in treatment T9, significantly enhance the nutritional quality of bottle gourd, offering a viable eco-friendly alternative to conventional cultivation methods.