Ultrasound and microbubbles have been widely demonstrated to accelerate the breakdown of blood clots, but the mechanisms of treatment require further investigation. In particular, there is a need to clarify the effect on the fibrin matrix—the insoluble polymer mesh that determines a clot’s integrity and mechanical properties. The objective of this in vitro study was to observe in real-time the mechanisms of microbubble-enhanced sonothrombolysis at the microscale. Fluorescently labeled porcine plasma clots were prepared on a glass coverslip and exposed to different types of microbubbles with or without the fibrinolytic agent recombinant tissue plasminogen activator. A 1 mm thick piezoelectric element was coupled with the glass substrate and driven at the resonant frequency of the system (1.9 MHz), with a duty cycle of 5% and a 0.1 Hz pulse repetition frequency. The acoustic field within the clot was characterized using a fiber optic hydrophone. Changes in the fiber network were monitored for 30 min by confocal microscopy.