In order to determine the effects of water deficit stress, nitrogen fertilization and zeolite on chlorophyll fluorescence, pigments, trigonelline content and seed yield in, a split factorial experiment was laid out in a randomized complete block design with three replications. Five irrigation regimes were randomly applied to the main plots. Subplots included six treatments and consisted of a factorial combination of three nitrogen fertilization (untreated plots, vermicompost at a rate of 2.7 ton ha^-1 and nitrogen chemical fertilizer at a rate of 11 kg.ha^-1) and two zeolite rates (0 and 9 ton.ha^-1). The results demonstrated that (F_m), (F_v), (F_v/F_m), chl a, b, total chl content and also seed yield were significantly reduced by water deficit stress, wheras minimum fluorescence (F₀), carotenoid and trigonelline concentrations were increased. In addition, the highest F_v/F_m, chl a+b content and the lowest F₀ and carotenoids were observed when irrigation was done after unloading 40% of ASW. In most treatments vermicompost increased the yield (by 25.51% and 98.32% in 2014 and 2015, respectively) and grain trigonelline concentration (7.46% in 2014) in Fenugreek. Mild water stress with vermicompost treatment is recommended for the production of trigoneline from Fenugreek seeds.