The crater lake of El Chichón active volcano represents one of the most important extreme ecosystems in the world due to its high temperatures, low pH and the appearance of high concentrations of heavy metals because of volcanic activity. The latter is of great importance in nearby volcano sites due to heavy metal pollution, which is one of the worst types of environmental problems in the world. In this study, the concentration of heavy metals was evaluated in soils and sediments from different sections in the crater lake of El Chichón volcano. Representative samples were collected from four sediments and soils in 2015 and 2017. These samples were analyzed for 20 metals by inductively coupled plasma-optical emission spectrometry (ICP-OES). The most abundant elements in sediments of the crater lake of “El Chichón” volcano were Fe, Na, Si, Ca, K and Al and not found in soil samples. Be and Tl were more abundant in the soil, but the concentration of Se was higher in soil without showing statistically significant differences. Principal component analysis (PCA) showed that the abundance of metals was influenced by sample type. That is, a higher concentration of heavy metals and trace elements was found in volcanic sediments as compared to soil samples. This difference may be related to metals originating from the magma, which is partially transported in the water stream that gives way to the volcano lake. The most toxic heavy metals identified and quantified in high concentrations in crater soils and sediments were As and Cd. This study suggests that sediments and soils of El Chichón crater lake could be an important source of heavy metals and toxic elements such as As and Cd.