Background: The sacha inchi plant contains nutrients that are beneficial for health, cosmetics, and food products, so it has the potential to be developed economically. The development of sacha inchi involves agricultural technology, which includes the treatment of fertilizer types that need to be studied in maintaining production and productivity. Objectives: This study aims to analyze the optimal type of fertilizer treatment on crop yields and the influence of farmers’ perceptions of socio-economic factors in the development of sacha inchi plants so that an optimal sacha inchi development prediction model is formed. Methods: The partial least squares structural equation modeling (PLS-SEM) method was applied in the study to analyze the effect of perception of socio-economic factors, and the adaptive neuro-fuzzy inference system (ANFIS) method was applied to predict the optimal fertilizer treatment model. Findings: The results of the PLS-SEM analysis showed that farmers’ perceptions of sacha inchi cultivation considered economic factors at a percentage of 50.66% and social factors at a percentage of 49.33% and had a linear relationship with the economic development of sacha inchi with a value of 0.832, although simultaneously, 77.7% was influenced by economic factors and social factors, and 22.3% was influenced outside these two factors. The ANFIS prediction results reinforced the results of the analysis, which stated that fertilizer treatment based on sacha inchi plant waste in the form of seed shells produced greater harvest weight compared with goat manure fertilizer. If farmers wanted to use a combination fertilizer, the used composition was 80% sacha inchi seed shell waste and 20% goat manure fertilizer or other materials; if the used composition was otherwise, the yield tended to decrease. This research contributes to the theory of production sustainability by integrating the optimal fertilization factor as a decision support unit in the model. Practically, this study recommends the application of fertilizer from the basic ingredients of sacha inchi seed shells to create a sustainable sacha inchi processing industry that ensures production stability, strengthens the agribusiness ecosystem, and develops the economic potential of sacha inchi and reduces the operational costs of sacha inchi farming by reducing the cost of purchasing fertilizer and supporting the circular economy model.