Productivity of medicinal and aromatic plants refers to their biomass and the target chemical constituents' quantity. A 2‐yr field study was laid out as a split‐plot to evaluate the effectiveness of the exogenous chitosan and fertilizer type on biomass, biochemical characteristics, and phenolic compounds of Thymus daenensis Celak. (denaian thyme, from the mint family). Mainplots consisted of fertilizer type, including synthetic fertilizer (Syn), cow manure (CM), vermicompost (VC), and a combined fertilizer. Foliar application of chitosan at three concentrations (0, 200, and 400 mg L–1) was allocated to subplots. Thyme responded differently, based on its stage of growth. In the establishing year, Syn, and 400 mg L–1 chitosan produced 2,047 kg ha–1dry matter. In the harvesting year, maximum biomass (2,853 kg ha–1) was obtained from the combined fertilizer and 400 mg L–1 chitosan. Accumulation of nutrients was in the order of K > N > P. The highest nutrient accumulation was obtained when combined fertilizer was used. Exogenous chitosan at the rate of 400 mg L–1 boosted nutrient density in leaves. Inboth growing seasons, all phenolic compounds were influenced by fertilizer and chitosan application. Cinnamic acid and rosmarrenic acid were the major phenolic compounds. In the establishment year, major and minor phenolic compounds were highest when CM was applied. Phenolic compounds reached their peak concentration in the harvest year in combined fertilizer treatment. The interactive effects of fertilizer and chitosan on phenolic compounds were minimal in both growing seasons. Combined organic and Syn and chitosan seemed an effective strategy to improve biomass yield, phenolic compounds, and nutrient density in thyme.