Complexation of micronutrients with complexing agents reduce undesirable reactions of fertilizers in soil water system. In the form of complex structure nutrients remain available to plants in the useable form. Nanoform fertilizer enhances the surface area of particles and less amount of fertilizer contact with large area of plant roots which reduce fertilizer cost. Controlling release of fertilizer using polymeric material like sodium alginate makes agriculture practices more efficient and cost effective. Several fertilizers and nutrients are used at a large scale to improve crop yields globally and almost more than half goes to waste. Therefore, there is a dire need to improve plant-available nutrients in soil, using feasible, environmentally friendly technologies. In the present research, complexed micronutrients were successfully encapsulated using a novel technique at nanometric scale. The nutrients were complexed with proline and encapsulated using sodium alginate (polymer). Sweet basil was subjected to seven treatments over three months in a moderately controlled environment (25 °C of temperature and 57% of humidity) to study the effects of synthesized complexed micronutrient nano fertilizers. The structural modifications of the complexed micronutrient nanoforms of fertilizers were examined, through X-ray powder diffraction (XRD) and scanning electron microscopy (SEM). The size of manufactured fertilizers was between 1 and 200 nm. Fourier transform infrared (FTIR) spectroscopy stretching vibration peaks at 1600.9 cm−1(C=O), 3336 cm−1(N–H) and at 1090.2 cm−1(N–H in a twisting and rocking) corresponds to the pyrrolidine ring. Gas chromatography–mass spectrometry was used to analyze the chemical makeup of the essential oil of the basil plants. Essential oil yield of basil plants increased from 0.0035 to 0.1226% after treatments. The findings of the present research show that complexation and encapsulation improve crop quality, essential oil yield, and antioxidant potential of basil.