Using plant byproducts as bioactive sources for in ovo injection (IOI) can enhance embryo development. This study evaluated the effects of air cell IOI of sweet orange peel (SP), pomegranate peel (PP), and olive leaf (OL) aqueous extracts on embryonic days 10 and 18, assessing chicken hatching and post-hatch performance up to 42 days of age. Nine hundred eggs were assigned to 10 treatments. Each treatment had three replicates (n = 30 eggs/replicate) with a 5 × 2 factorial design (uninjected negative control, injection with distilled water as positive control, or injection with 1% SP, PP, or OL on day 10 or 18 of embryogenesis). Compared to the negative control, the results revealed that in ovo-injected substances (IOSs) did not alter hatchability but significantly decreased pipped-chick percentage, the heterophil-to-lymphocyte ratio, malondialdehyde, cholesterol, triglycerides, and glucose levels. However, IOSs were found to increase superoxide dismutase (SOD) levels, liveability, and final body weight. Specifically, SP maximised hatch weight, gut length, and thymus weight, whilst decreasing eggshell conductance and uric acid. SP and OL reduced liver enzyme activities, whereas PP lowered creatinine. Compared to day 10, IOI on day 18 improved hatchability, packed cell volume, SOD activity, liveability, and organ development. In conclusion, IOI with SP or OL, particularly on day 18 of incubation, is recommended to improve antioxidant status, biochemical indices, and cumulative body weight.