Polymeric nanoparticles have emerged as carrier systems for molecules that release nitric oxide (NO), a free radical involved in plant stress responses. However, to date, nanoencapsulated NO donors have not been applied to plants under realistic field conditions. Here, we verified the effects of free and nanoencapsulated NO donor, S-nitroso-mercaptosuccinic acid (S-nitroso-MSA), on growth, physiological and biochemical parameters of neotropical tree seedlings kept under full sunlight in the nursery for acclimation. S-nitroso-MSA incorporation into chitosan nanoparticles partially protected the NO donor from thermal and photochemical degradation. The application of nanoencapsulated S-nitroso-MSA in the substrate favoured the growth of seedlings of Heliocarpus popayanensis, a shade-intolerant tree. In contrast, free S-nitroso-MSA or nanoparticles containing non-nitrosated mercaptosuccinic acid reduced photosynthesis and seedling growth. Seedlings of Cariniana estrellensis, a shade-tolerant tree, did not have their photosynthesis and growth affected by any formulations, despite the increase of foliar S-nitrosothiol levels mainly induced by S-nitroso-MSA-loaded nanoparticles. These results suggest that depending on the tree species, nanoencapsulated NO donors can be used to improve seedling acclimation in the nursery.