Abstract: Background and Objective: The need for functional food is increasing along with the increase in population. Meanwhile, Indonesia experiences the conversion of agricultural land into non-agricultural land reaching 120,000 ha per year. Therefore, one of the cultivation methods for the development of functional food crops is the intercropping system. To support soil fertility, various organic fertilizers are used, namely cow manure, chicken manure and municipal compost. The purpose of this study was to evaluate the efficiency of the intercropping system of sweet corn and vegetable soybeans in the application of the combination of different organic fertilizer sources and dosage of NPK fertilizer. Materials and Methods: The research was carried out from June to August, 2022 in the Giwangan Umbulharjo Village, special region of Yogyakarta. The study was arranged in a factorial randomized complete block design with three replications. The first factor was the source of organic fertilizer consisting of three sources (cow, chicken manure and municipal compost) and the second factor was dosages of NPK consisting of three levels 200, 300 and 400 kg ha–1, so that obtained 27 unit of experimental plots. The observation variable includes components of growth, yield and efficiency of land. The Analysis of Variance (ANOVA) at a significant level of 5% was used to analyze the significant differences between treatments, followed by Duncan’s Multiple Range Test at a significant 5%. Results: The application of a combination of chicken manure with a dosage of 300 kg ha–1 NPK fertilizer in the best growth and the highest yield of intercropping sweet corn and vegetable soybeans and the component efficiency land showed the value of land equivalent ratio, competition index, crop system efficiency and actual yield total. Conclusion: The intercropping system of sweet corn and soybeans could increase the productivity of both crops and improve land efficiency, including land equivalence ratio, competition index, crop system efficiency and total yield. Cow manure or municipal compost combined with NPK fertilizer at 300 kg ha–1 could improve the yield of corn and soybean.