The primary aim of this work was to study the diseased and healthy rice plant samples at the elemental and molecular level to get the proper understanding of the causes and the chemical changes occurred in the healthy rice grains with the infestation due to false smut disease. We have used microscopic and isolation methods to detect and identify the presence of the species of pathogen involved in the diseased rice plant samples. Elemental analyses of rice grains were carried out using laser-induced breakdown spectroscopy (LIBS) and wavelength dispersive X-ray fluorescence (WDXRF) spectrometry. This revealed the mineral changes appeared in diseased rice plant samples due to the invasion of pathogens. The results from LIBS and WDXRF showed that the mineral elements such as calcium (Ca), magnesium (Mg), silicon (Si), copper (Cu) and iron (Fe) decreased in diseased rice grains than those of healthy rice grains whereas some elements showed their variable behavior in diseased rice grains than those of healthy grains. The results obtained by LIBS is in close agreement with the results obtained by WDXRF. We have employed Fourier-transform infrared (FTIR) spectroscopy to study the molecular changes appeared in the active bio compounds of the rice grains due to the infection caused by false smut. The present spectroscopic studies would provide the proper understanding of the rice false smut disease and also help in developing the proper treatment strategies to prevent the further yield loss caused by the rice false smut disease.