Papaya is a tropical fruit of the Carica papaya plant and grown all over the world. Root knot nematodes are one of the major problems in papaya fruit crop production and causes maximum yield loss every year by slowly killing the plant. In this article, we study healthy as well as nematode-infested papaya plants at the atomic and molecular levels to obtain information about the causes and changes occurring in the plant after infestation. Microscopic observations were made to check the presence of pathogens in the plant. Elemental profiling of healthy and infested papaya plants was assessed by using two advanced spectroscopic techniques, namely laser-induced breakdown spectroscopy (LIBS) and wavelength dispersive X-ray fluorescence spectroscopy (WDXRF). The structural changes in the complex bio compounds, such as starch, protein, lipids, fatty acids, and carbohydrates, were assessed by Fourier transform infrared spectroscopy (FTIR). The elemental and molecular profiling results of the infested vs. the healthy papaya plants were compared to establish why the plants die.