A study using random forest (RF) algorithms and principal component analysis (PCA) was proposed to identify the effects of arbuscular mycorrhizal fungal inoculation, the seed maturation stage and the geographic diversity of Pimpinella anisum L. accessions on the physicochemical composition of seeds. Seeds of six anise varieties from North African and Middle Eastern accessions were inoculated or not inoculated with AMF (an arbuscular mycorrhizal fungus) and then grown under controlled conditions. Seeds were harvested at three different maturity stages: mature seeds (157 d after sowing), premature seeds (147 d after sowing), and immature seeds (137 d after sowing). Forty-nine variables related to physical properties, total nutrients, metabolic compounds, essential oils, and biological activity were measured in P. anisum seeds.