Heading leafy vegetables (HLVs) are essential horticultural crops that feed many people worldwide. An increasing global population demands more cropping systems, leading to stresses such as fertilizer overuse and soil salination, decreasing in crop productivity and agricultural sustainability. Hence, developing those eco-friendly farming strategies that could simultaneously reduce fertilizer usage and increase crop harvest is urgent for agriculture. An endophytic bacterium Burkholderia seminalis 869T2 with pyrroloquinoline quinone (PQQ) producing ability were applied as biostimulant for vegetable seedlings under greenhouse or field conditions. Two globally important HLVs, cabbage and head lettuce, were preliminarily tested, and further examinations under in-field farming during two different seasons were carried out to develop an endophytic biostimulants (EBs)-assisted lettuce production system. In this study, we confirmed that B. seminalis 869T2 is versatile EBs for HLVs, which significantly promote plant growth and enhance the qualities of crops by increasing the harvested head weight, size and nutrient composition. Nevertheless, the harvest was accelerated by two weeks, together with higher product qualities and 50% fertilizing cost savings per hectare. Our study provides an in-field EBs-assisted management for lettuce production that could decrease costs and increase the product’s value. The results highlight the importance of endophytic bacteria that deserve further investigation due to their enigmatic symbiotic relationships with their hosts and potential usage in the agro-industry.