The present study was carried out to valorize the Opuntia ficus-indica (OFI) by-products by extracting and identifying their biochemical compounds and evaluating their antioxidant potential by in vitro activities (DPPH radical and FRAP), as well as their capacity to stabilize margarine oxidation (rancimat test). In addition, their in vitro anticoccidial effect on the destruction of Eimeria oocysts isolated from naturally infected chickens was also targeted. Microwaves and response surface methodology tools were used to extract the maximum amount of phenolic compounds (42.05 ± 0.46 GAE mg/g DW of total phenolic compounds in 90 s at 400 watts). Moreover, the effect of extraction factors was also studied. Eight phenolic compounds, including isorhamnetin, dihydrokaempferol, and kaempferol-3-O-rutinoside, were identified. The findings confirmed that OFI peel extract has strong antioxidant activities (DPPH radical, ferric reducing power). The rancimat test shows that OFI peel extract improves margarine stability by 3.2 h. Moreover, it has a notable destruction rate of Eimeria oocysts (30.06 ± 0.51%, LC₅₀: 60.53 ± 0.38 mg/mL). The present investigation offers promise for the reuse of food waste as natural margarine additives, protection of the environment, and substitution of anticoccidial synthetic treatments.