Aims <p>Green organic vegetables are highly valued for their rapid growth and high nutritional value. However, manure application can pose a risk of promoting the accumulation of antibiotic resistance genes (ARGs) in vegetables. ARGs in the phyllosphere of vegetables can be removed by washing, but the effect of light intensity on the enrichment of resistance in the leaf endophytes remains unclear.</p> Methods <p>Lettuce was cultivated under different light intensities with manure application. Environmental factors, the abundance of ARGs in samples, and microbial sequencing were determined to explore the enrichment characteristics and source pathways of ARGs in the leaf endophytes of lettuce under different light conditions.</p> Results <p>Under both high and low light conditions, amending soil with chicken manure enhanced the abundance of ARGs in soil and root endophytes but reduced in leaf endophytes and phyllosphere. Co-occurrence network indicated that the positive correlation between the ARGs of leaf endophytes and those in phyllosphere was as high as 93.88%, which was higher than that between leaf endophytic ARGs and those in soil or root endophytes. Under manure application, high light intensity reduced the proportion of ARGs in leaf endophytes by 2.75% compared with low light intensity. The ARGs of leaf endophytes were mainly influenced by microorganisms, and random forest analysis revealed that <i>Bacteroidetes</i> played a key role. Notably, the combined treatment of high light and manure increased lettuce yield.</p> Conclusions <p>The combined treatment of high light and manure is a viable agronomic strategy to reconcile food safety and high crop productivity.</p>