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Dry powder extracts are the most suitable pharmaceutical forms of phytomedicines due to their greater physical and chemical stability in the solid state, in addition to the possibility of easy preparation of tablets and capsules. Recently, Baccharis dracunculifolia D.C. crops have been stimulated in Brazil to obtain the green propolis, which is derived from pollen harvesting of Baccharis by the Apis mellifera, and develop new phytomedicines from this plant. The aim of this work was to obtain stable powdered Baccharis dracunculifolia leaf extracts dried by fluidized-bed atmospheric spray-freeze-drying and study the stability of its chemical markers in the solid state. The drying was performed using D-mannitol, modified corn starch and their mixture as adjuvants. Physical characterization was performed by determining the dried extract powder size, morphology, flow and packing. Their chemical stability was evaluated by high performance liquid chromatography quantification of p-coumaric acid, cinnamic acid, artepillin C and baccharin. The antioxidant activity of the dried extract was determined using the stable free radical 2,2-diphenylpicrylhydrazil. The results showed that the four prenylated compounds are sensitive to drying at freezing temperatures, but D-mannitol could efficiently prevent their loss. The Baccharis spray-freeze-dried extracts showed a high yield, low moisture and excellent pharmacotechnical properties. The stability tests demonstrated a high loss of polyphenols at 40, 60 and 80 °C, especially artepillin C (the main marker) and showed high instability. The kinetics of polyphenols losses were measured, and their rates were used to fit three-dimensional diffusion models and the Arrhenius equation. The results demonstrate that the Baccharis dracunculifolia dried extract, using artepillin C as a reference, could achieve a shelf life as long as 10 years when stored at 4 °C and protected from light. The process of fluid-bed atmospheric spray-freeze-drying was shown to be an attractive alternative for drying of heat-sensitive and high value-added materials such as medicinal plant extracts.