A new analytical method using micro-X-ray fluorescence (XRF) is presented for the in situ analysis of major elements in rock samples. This approach has allowed for a separate study of hydrothermal alteration of matrix versus fragments in volcaniclastic material (i.e. flow breccia). This is particularly important for volcanogenic massive sulfide (VMS) exploration in subaqueous felsic dome-flow complexes, where brecciated facies are omnipresent and the imprint of hydrothermal alteration is typically heterogeneous. In this study, eleven elements are measured with a 1.7 by 1.3 mm window considered to be representative of each sample, based on replicate analyses. An average is calculated for the analyzed window and yields a nearly complete analysis with the exception of loss of ignition (LOI). Micro-XRF data were validated using whole rock XRF analyses performed on the same sample block. The application of this chemical method has been tested successfully on thin sections from the Cap d'Ours section of the Glenwood rhyolite in the Rouyn-Noranda region of Québec, Canada. With 58 samples spaced at approximately 50 m intervals, two styles of alteration zoning were recognized: (1) a lateral and concordant zoning expressed by vent-proximal silicification in the west grading toward vent-distal chlorite–sericite alteration to the east, and (2) vertical and discordant zoning expressed by stronger sericitization in the upper part of later volcanic quartz- and feldspar-phyric endogenous lobes. The former is typical of cooling induced by seawater interaction at the lava–water interface at temperatures greater than 400 °C, whereas the latter is related to lower temperature (< 300 °C) hydrothermal mineralization associated with endogenous lobe emplacement within the volcanic pile. The presented results clearly demonstrate the potential use of the micro-XRF data for characterizing weak to intense hydrothermal alteration in highly fragmented volcanic rocks.