<p>Filamentous fungi play crucial roles in global carbon and nutrient cycling, soil carbon sequestration, agricultural soil management, contaminant fate and transport, biofouling of engineered materials and human health. Although these processes typically involve multiple fluid phases in porous media, the mechanisms by which fungi regulate fluid flow remain poorly understood, limiting our ability to predict and harness fungus-mediated processes. The complexity and opacity of porous media further obscure our understanding of how fungi influence fluid flow and distribution. Here we explore the impact of filamentous fungi on multiphase flow and fluid redistribution using a dual-porosity microfluidic chip, featuring a flow channel embedded within tight porous media. Our pore-scale visualizations show that filamentous fungi can actively induce multiphase flow and mobilize trapped fluid phases in porous media through localized clogging and hyphal-induced pore invasion, enhancing the oil–water interfacial area and redistribution of fluid phases. This study reveals the mechanisms by which filamentous fungi modulate fluid flow and distribution, offering insights into harnessing fungal processes to enhance applications such as bioremediation and carbon sequestration.</p>