Under climate change threats, there is a growing need to adapt the conventional agronomic practices used in rainfed olive orchards by sustainable practices, in order to ensure adequate crop yield and olive oil quality and to preserve soil health. Therefore, for two years, the effects of conventional tillage practice (T) and two sustainable soil management strategies, a leguminous cover crop (LC) and its combination with natural zeolites (ZL), on the yield, fatty acid composition, polyphenolic profile and quality indices of olive fruits and oil were evaluated. Crop yield was significantly increased by LC and ZL in the first year. Although in the second year no significant differences were verified, the cumulative yield increased significantly by 31.6% and 35.5% in LC and ZL trees, respectively. LC enhanced the moisture and size of olives, while ZL increased, in general, the concentrations of oleuropein, verbascoside, caffeic acid and epicatechin, as well the oleic/linoleic ratio in fruits and the levels of 3,4-dihydroxyphenylglycol, tyrosol, verbascoside and caffeic acid in olive oil. Despite the higher concentration of total phenols in the fruits and oil from T trees in the warmer and dryer year, the quality of the oil decreased, mainly when compared with ZL, as evidenced by the peroxide value and K232 and K270 coefficients. In short, both sustainable soil management strategies appear to be promising practices to implement in olive orchards under rainfed conditions, but the innovative strategy of combining zeolites with legume cover crops, first reported in the present study, confers advantages from a nutritional and technological point of view. Nevertheless, studies subjected to the long-term use of these practices should be conducted to ensure the sustainability of the crop yield and olive oil quality.