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Agroforestry systems have been practiced for hundreds of years with multiple benefits both environmentally and economically in terms of productivity. Olive cultivation is widespread in the countries of the Mediterranean basin, including Greece. Agroforestry practices are common in olive groves, but little research has been conducted on the productivity of such systems, especially with medicinal–aromatic plants (MAPs) as understory crops. Natural populations of MAPs can be found in various ecosystems, while some of them are cultivated. The purpose of this research was to study the effects of fertilization and shading both on yield and chemical composition of essential oils derived from chamomile (Matricaria recutita L.) and anise (Pimpinella anisum L.), grown in olive silvoarable systems. Fertilization and shading increased the plant height of chamomile and delayed the flowering. In addition, fertilization increased the concentration of α-bisabolol oxide A and (Z)–spiroether, and reduced the α-bisabolone oxide A and hamazulen. Shade also reduced α-bisabolone oxide A and hamazulen but increased the α-bisabolol oxide B. In the case of anise, fertilization increased plant height, decreased the concentration of limonene, and increased the concentration of E-anethole. Shading reduced plant height. Intercropping of olive trees with chamomile and anise yielded essential oils rich in the substances defined by the commercial specifications.