Plastids develop into nutrient-storing leucoplasts in seeds and roots. Efficient protein delivery is essential to modify biosynthetic processes in leucoplasts for human needs, but no effective transit peptide for leucoplasts is currently available. Using an in vitro leucoplast import system, we have identified six high-efficiency transit peptides. Compared to a widely used chloroplast transit peptide, these peptides delivered comparable amounts of GFP into chloroplasts, but 2-7 times more GFP into root and petal leucoplasts, attesting to the advantage of screening using leucoplasts. When used to deliver bacterial phytoene synthase (crtB) into rice calli and glyphosate-resistant EPSP synthase into Arabidopsis, these peptides enhanced carotenoid production and herbicide resistance, respectively. The correlation among levels of GFP delivery, carotenoid production and herbicide resistance indicate that the efficiency of these transit peptides is consistent across plant species and passenger proteins. Therefore, transit peptide selection offers an effective way to modulate production levels of engineered proteins.