Amorphous molybdenum sulfide (a-MoS x ) is a promising candidate to replace noble metals as electrocatalysts for the hydrogen evolution reaction (HER) in electrochemical water splitting. So far, understanding of the activity of a-MoS x in relation to its physical (e.g., porosity) and chemical (e.g., Mo/S bonding environments) properties has mostly been derived from bulk electrochemical measurements, which provide limited information about electrode materials that possess microscopic structural heterogeneities. To overcome this limitation, herein, scanning electrochemical cell microscopy (SECCM) has been deployed to characterize the microscopic electrochemical activity of a-MoS x thin films (ca. 200 nm thickness), which possess a significant three-dimensional structure (i.e., intrinsic porosity) when produced by electrodeposition. A novel two-step SECCM protocol is designed to quantitatively determine spatially resolved electrochemical activity and electrochemical surface area (ECSA) within a single, highthroughput measurement. It is shown for the first time that although the highest surface area (e.g., most porous) regions of the a-MoS x film possess the highest total activity (measured by the electrochemical current), they do not possess the highest specific activity (measured by the ECSA-normalized current density). Instead, the areas of highest specific activity are localized at/around circular structures, coined "pockmarks", which are tens to hundreds of micrometers in size and ubiquitous to a-MoS x films produced by electrodeposition. By coupling this technique with structural and elemental composition analysis techniques (scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray photoelectron spectroscopy) and correlating ECSA with activity and specific activity across SECCM scans, this work furthers the understanding of structure−activity relations in a-MoS x and highlights the importance of local measurements for the systematic and rational design of thin film catalyst materials.