Organic fertilization and crop association are two agroecological management practices that have the potential to optimize land use in horticultural production. The objective of this study was to evaluate the effect of Bokashi and Bokashi amended with Vermicompost Leachate (VL) on the growth, yield and quality of jalapeño pepper (Capsicum annuum L.) and onion (Allium cepa L.) in monoculture and intercropping cultures. This work was conducted under rainfed conditions in the community of Santa Rosa el Oriente, a municipality of Trinity, Chiapas. A randomized complete block design in a split plot arrangement with six treatments and four replicates by treatment was used. Bokashi significantly increased the number of leaves and plant height in onion (37 and 62%) and jalapeño pepper (133 and 94%) compared with the control plants. In jalapeño pepper and onion, the content of capsaicin and soluble solids was 41 and 42% higher with the application of Bokashi plus VL, respectively. In onion, Bokashi increased the polar and equatorial diameters and bulb weight by 28, 69 and 269%, respectively, and its yield increased from 6.4 to 21.0 t ha-1. The land equivalent ratio (LER) was 1.34 to 1.55, which indicated that intercropping was advantageous on monoculture, regardless of the fertilization type. Therefore, the application of Bokashi and crop association favored the yield and quality of jalapeño pepper and onion with an efficient use of the land.