The present work contains the first microstratigraphic study of a shell midden located on the hyperarid coast of the Atacama Desert (Chile), Pacific coast of South America. We combined micromorphology with faunal data from the Middle Holocene shell midden site of Zapatero to understand site formation processes from a dual geoarchaeological and zooarchaeological perspective. Geoarchaeological methods included soil micromorphology, Fourier Transform Infrared Spectrometry (FTIR) and micro-FTIR. This combined approach identified three main moments of formation and occupation at Zapatero: one starting around 7000 cal yr BP, when successive centimetre-thick layers of predominantly shellfish were continuously accumulated; a second moment between 6600 and 6400 cal yr BP, when decametric layers of fish bones and shellfish remains were intermittently deposited; and a third and final moment that is characterized by the complete reworking of the shell midden, possibly by a tsunami that affected the north of Chile about 4000 years ago. Micromorphological data provided paleoclimatic information from the Middle Holocene to the present time, with evidence of drier conditions during the first moment of formation/occupation, and more humid conditions during the second and third moments. It also revealed a larger abundance of decayed fish bones than what was indicated by faunal analysis, suggesting potential taphonomic pathways for the faunal remains. The micro-components identified in the third moment of formation/occupation offer complementary evidence to support the tsunami hypothesis affecting the upper layers at Zapatero.