We analyzed the toxic effect of the ethanolic extract of Passiflora incarnata (EEP) and its nanoformulation (N-EEP) in the in vitro and in vivo models (zebrafish embryos and Swiss albino mice). The EEP composition was verified by phytochemical and GC–MS analysis. The synthesized N-EEP was characterized using UV–visible spectroscopy and scanning electron microscopy. In vitro results showed both EEP and N-EEP have a dose-dependent effect in L132 cells (normal embryonic lung cells). In zebrafish embryos, no developmental changes were observed for both EEP and N-EEP at 200 µg/ml. The acute and sub-acute toxicity of EEP and N-EEP was identified by oral administration in Swiss albino mice. A single-day oral dose of EEP and N-EEP at different concentrations was administered for acute toxicity, and changes in body weight, food, water intake, temperature, respiration rate, skin color changes, and eye color till 72 h was observed. In a sub-acute toxicity study, 28 days oral administration of different concentrations of EEP and N-EEP was done. Hematological analysis, serum hepatic biochemical parameter analysis, and histopathological analysis for the liver, kidney, spleen, intestine, and heart were performed. The results indicated that lower than 600 mg/kg of EEP and N-EEP can safely be used for the remediation of a spectrum of diseases.