Herein, we report a facile, economic, one-pot green synthesis of zinc oxide nanoparticles (ZnO-NPs) for diverse biomedical applications. In the study, ZnO-NPs were synthesized using an aqueous extract of Aquilegia pubiflora as an effective reducing and capping agent. The biomediated nanoparticles were characterized using various techniques including high-performance liquid chromatography (HPLC), X-ray diffraction, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy, Dynamic light scattering, photoluminescence, and RAMAN. The particles were highly pure, having an average size of 34.23 nm with spherical or elliptical morphology, and displayed good aqueous dispersion capability. FTIR and HPLC confirmed the successful capping of flavonoids and hydroxycinnamic acid derivatives. The characterized NPs were then explored for their antimicrobial and anti-leishmanial potential. Among the tested bacterial and fungal strains, ZnO-NPs were more potent toward Pseudomonas aeruginosa and Fusarium solani with inhibition zone of 10.3 ± 0.19 mm and 13 ± 1.4 mm, respectively. A dose-dependent cytotoxic effect was observed against Leishmania tropica (KWH23) with significant IC 50 for both the promastigote (48 µg/mL) and amastigote form (51 µg/mL) of the parasite. In addition, bacterial kinase enzymes were inhibited by ZnO-NPs, thus allowing us to elaborate a possible action mechanism. Finally, the remarkable biocompatible nature of the particles was confirmed against freshly isolated human red blood cells (hRBCs). Altogether, these results affirmed the high antimicrobial and antiparasitic potential of ZnO-NPs obtained through a biogenic synthetic approach using aqueous extract of the Himalayan Columbine (Aquilegia pubiflora).