Agaricus subrufescens Peck is a basidiomycete with immunomodulatory compounds and antitumor activities. This research evaluated the mycochemical composition of A. subrufescens, considering their morphological and physiological stage of maturity, with a particular focus on the development of a traceability process for the formulation of new nutritional products based on fungal foods. The stipes contained a high amount of dry matter (10.33%), total carbohydrate (69.56%), available carbohydrate (63.89%), and energy value (363.97 kcal 100 g−1 DM). The pilei contained a high amount of moisture (90.66%), nitrogen (7.75%), protein (33.96%), ash (8.24), crude fat (2.44%), acid detergent fiber (16.75 g kg−1), neutral detergent fiber (41.82 g kg−1), hemicellulose (25.07 g kg−1), and lignin (9.77 g kg−1). Stipes with mature physiological stage had higher values of dry matter (10.50%), crude fiber (5.94%), total carbohydrate (72.82%), AC (66.88%), and energy value (364.91 kcal 100 g−1 DM). Pilei of the mushrooms in the immature physiological stage had higher values of P (36.83%), N (8.41%), and A (8.44%). Due to the differences between the mycochemical compositions of the morphological parts of mushrooms linked to their physiological stage of maturity, such characteristics have immense potential to be considered for a traceability process. This study can be used for the purpose of providing the consumer with more product diversity, optimizing bioactivities of composts, and allowing farmers an efficient and profitable use of the mushroom biomass.