Eggshell wastes are one of the main solid wastes due to the consumption of eggs in daily diets and the general way of disposal for eggshell is in landfills that would lead to pollution and public health. To reduce negative impacts on the environment, eggshell wastes have been found to be used as a bio fertilizer in agriculture. In Malaysia, the local production of bird’s eye chili, or called cili padi (Capsicum frutescens) in large scale is still relatively low even though it is frequently used as spice in daily cooking. In order to determine the best fertilization formula for eggshell wastes in order to improve plant growth and yield, this study examined the effects of varying amounts of eggshell powder, also known as ESP (0 g, 45 g, 60 g, 75 g, and 90 g), on bird’s eye chilli using the soil’s pH value, soil nutrients, morphological analysis, and metabolite analysis. Following ESP application, the pH of the soil remained acidic in all treatments. 90 g with 60.43% was the optimal ESP formulation in terms of growth rate for plant height. When it came to increasing the number of leaves, the 45 g ESP formulation yielded the best results (382.36%), while the 60 g ESP formulation was the most effective in growing the number of branches (379.17%) and nodes (80.14%). For flowering and fruit yield, the highest number was formulated by 75 g ESP, that was 8 and 6, respectively. The total chlorophyll content (30.723 mg/mL) and total phenolic content (0.414 ± 0.01 mg GAE/g extract) had the highest value when applying 75 g ESP. The optimum formulation of eggshell wastes as bio fertilizer differs due to its differential effects on individual plant growth parameters. The formulation of 90g ESP was the best formulation that mostly highlighted the improvement in most parameters such as the plant height and metabolite (chlorophyll and total phenolic content).