Nowadays, there is a high demand in many industrial countries for healthy foods and sustainable products and so to explore innovative food technologies, such as fortification with bioactive compounds such as antioxidants and polyphenols, that may be sourced from herbs or by-products. This study’s objective was to explore the fortification of refined olive oils with natural bioactive compounds such as the herbs rosemary (Rosmarinus officinallis, L.), basil (Ocimum basillicum, L.), sage (Salvia officinalis, L.), lemon balm (Melissa oficinallis, L.), St. John’s wort (Hypericum perforatum, L.), pink savory (Satureja thymbra, L.), dittany (Origanum dictamnus, L.), and by-products such as pomace from olives, olive leaves (Olea europaea, L.), orange peel (Citrus aurantium, L.), lemon peel (Citrus limon, L.), pomegranate peel (Punica granatum, L.), and mandarin peel (Citrus reticulata). The fortification of the refined olive oils was performed with the use of different methodologies such as conventional maceration (CM), incubation shaking maceration (ISM), and ultrasound-assisted maceration (UAM). Folin–Ciocalteau (FOLIN) and Ferric-Reducing Antioxidant Power (FRAP) assays were used to measure their total phenolic content and antioxidant capacity. All methods demonstrated that the temperature, sample concentration, and time of maceration are considered of high importance in the fortification of refined olive oil. In vitro digestion process showed the bioavailability of the antioxidant and phenolic compounds in the fortified olive oil that ranged from 4.84% to 53.11%. Furthermore, the refined olive oils fortified with pomace, basil, St. John’s wort, and pomegranate peel presented the highest antioxidant and phenolic predicted bioavailability indices during the in vitro process compared to the control refined olive oil. Finally, fortification with natural herbs or by-products can be considered an innovative method for the enhancement of the nutritional value of refined olive oils.