Salvia ceratophylloides (Ard.) is an endemic and rare plant species recently rediscovered as very few individuals at two different Southern Italy sites. The study of within-plant variation is fundamental to understand the plant adaptation to the local conditions, especially in rare species, and consequently to preserve plant biodiversity. Here, we reported the variation of the morpho-ecophysiological and metabolic traits between the sessile and petiolate leaf of S. ceratophylloides plants at two different sites for understanding the adaptation strategies for surviving in these habitats. The S. ceratophylloides individuals exhibited different net photosynthetic rate, maximum quantum yield, light intensity for the saturation of the photosynthetic machinery, stomatal conductance, transpiration rate, leaf area, fractal dimension, and some volatile organic compounds (VOCs) between the different leaf types. This within-plant morpho-physiological and metabolic variation was dependent on the site. These results provide empirical evidence of sharply within-plant variation of the morpho-physiological traits and VOCs profiles in S. ceratophylloides, explaining the adaptation to the local conditions.