Unravelling a chain of events in ultrasound-assisted extraction (UAE) of bioactive compounds from plants has to start with a detailed description of destructuration at macroscopic and microscopic scale. The present work aims to study the impacts and interactions of UAE on the extreme complexity and diversity of plants structures. Three plant species were selected for their difference in specialized structures and their spatial distribution of secondary metabolites: bitter orange leaf (C. aurantium L.), blackcurrant leaf (R. nigrum L.), and artichoke leaf (C. scolymus L.). Different microscopic techniques (Cyto-histochemistry, stereomicroscopic analysis, Scanning Electron Microscopy (SEM)) have been used to understand the complexity of plant structures and to highlight ultrasound-induced impacts especially on metabolites storage structures, with a neat comparison with conventional “silent” extraction procedure. The main results indicate that spatial UAE impacts are strongly related to plant structures’ properties (morphology, thickness, etc.) and particularly to the nature and the chemical constitution of their storage specialized structures. From a temporal point of view, for all studied leaves, observed mechanisms followed a special order according to structures and their mechanical resistance level to ultrasound (US) treatment. Microscopic mapping of metabolites and structures should be considered as a decision tool during UAE to target intensification process.