The implementation of nanotechnology in the field of plant tissue culture has demonstrated an interesting impact on in vitro plant growth and development. Furthermore, the plant tissue culture accompanying nanoparticles has been showed to be a reliable alternative for the biosynthesis of secondary metabolites. Herein, the effectiveness of zinc oxide nanoparticles (ZnONPs) on the growth of Delonix elata calli, as well as their phytochemical profiles, were investigated. Delonix elata seeds were collected and germinated, and then the plant species was determined based on the PCR product sequence of ITS1 and ITS4 primers. Afterward, the calli derived from Delonix elata seedlings were subjected to 0, 10, 20, 30, 40, and 50 mg/L of ZnONPs. The ZnONPs were biologically synthesized using the Ricinus communis aqueous leaf extract, which acts as a capping and reducing agent, and zinc nitrate solution. The nanostructures of the biogenic ZnONPs were confirmed using different techniques like UV–visible spectroscopy (UV), zeta potential measurement, Fourier transform infrared spectra (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM). Adding 30 mg/L of ZnONPs to the MS media (containing 2.5 µM 2,4-D and 1 µM BAP) resulted in the highest callus fresh weight (5.65 g) compared to the control and other ZnONP treatments. Similarly, more phenolic accumulation (358.85 µg/g DW) and flavonoid (112.88 µg/g DW) contents were achieved at 30 mg/L. Furthermore, the high-performance liquid chromatography (HPLC) analysis showed significant increments in gallic acid, quercetin, hesperidin, and rutin in all treated ZnONP calli compared to the control. On the other hand, the gas chromatography and mass spectroscopy (GC-MS) analysis of the calli extracts revealed that nine phytochemical compounds were common among all extracts. Moreover, the most predominant compound found in calli treated with 20, 30, 40, and 50 mg/L of ZnONPs was bis(2-ethylhexyl) phthalate, with percentage areas of 27.33, 38.68, 22.66, and 17.98%, respectively. The predominant compounds in the control and in calli treated with 10 mg/L of ZnONPs were octadecanoic acid, 2-propenyl ester and heptanoic acid. In conclusion, in this study, green ZnONPs exerted beneficial effects on Delonix elata calli and improved their production of bioactive compounds, especially at a dose of 30 mg/L.