The knowledge of the medicinal plants' organs containing a great number of bioactive compounds is of high importance. Thus, the need to study phytochemical compositions and biological activities of different organs of Zosima absinthifolia is highly demanding rather than any time before in the past. The essential oil was analyzed using GC and GC/MS. Total phenol and flavonoid content, and phenolic compound analysis were evaluated via spectrophotometry, and HPLC methods, respectively. Antioxidant, antibacterial, and cytotoxic activities were assayed by DPPH, disk diffusion, and MTT methods, separately. The results illustrated the maximum yield of essential oil was achieved at the late-mature/ripe seeds (0.88%), while the leaves had the lowest yield (0.31%). The essential oil analysis showed that octyl acetate and 1-octanol were the main compounds in the early development, mid-mature, and late-mature seeds. The highest total phenolic and flavonoid content were achieved in the acetone extracts of different seeds. Moreover, only caffeic acid and salicylic acid were detected in the ethyl acetate, acetone, and methanolic extracts, and the acetone extract of all aerial parts of the plant showed the maximum content. The biological results revealed that the highest antioxidant and cytotoxic properties were obtained in the acetone extracts of flowers and the early development stage of seeds. Acetone extract of all parts of the plant was highly active against Bacillus subtilis, B. pumilus, and Staphylococcus aureus bacteria. Finally, it can be inferred that the different organs and extraction solvents could influence the phytochemical compounds and biological properties of Z. absinthisfolia.