Flooding can damage the photosynthetic apparatus and initial growth of Schinus terebinthifolia. We aimed this study evaluates the potential of silicon (Si) and salicylic acid (SA) as mitigating agents on the ecophysiological responses and initial growth of S. terebinthifolia subjected to flooding periods. Seedlings were grown under the following conditions: 1) control (non-flooded): daily irrigation, 2) Flooded (F): storage of seedlings in a 500 L plastic pool, keeping the water depth at ± 2.0 cm above the substrate level, 3) F + 1.0 mM Si, 4) F + 2.0 mM Si, 5) F + 1.5 mM SA, and 6) F + 3.0 mM SA, and evaluated to 15 and 30 days. We observed that flooded seedlings formed hypertrophied lenticels on the stem on the 7th day as a stress adjustment strategy. S. terebinthifolia is sensitive to flooding, although it maintains a stable gas exchange for up to 15 days in this condition. The applications of 1.0 mM Si mitigated the pronounced decrease of gas exchange by 30 days. Using 1.0 mM Si and 3.0 mM SA contributed for integrity of the photosynthetic apparatus and to photochemical activities in the reaction centers, in addition favors to higher seedling biomass and quality under flooding. Foliar application of Si and SA is promising practice for photosynthetic metabolic and initial growth of S. terebinthifolia seedlings under flooded stress.