An interface between two miscible fluids is transient, existing as a non-equilibrium state before complete molecular mixing is reached. However, during the existence of such an interface, which typically occurs at relatively short time scales, composition gradients at the boundary between the two liquids cause stresses effectively mimicking an interfacial tension. Here, we combine numerical modelling and experiments to study the influence of an effective interfacial tension between a colloidal fibre dispersion and its own solvent on the flow in a microfluidic system. In a flow-focusing channel, the dispersion is injected as core flow that is hydrodynamically focused by its solvent as sheath flows. This leads to the formation of a long fluid thread, which is characterized in three dimensions using optical coherence tomography and simulated using a volume of fluid method. The simulated flow and thread geometries very closely reproduce the experimental results in terms of thread topology and velocity flow fields. By varying the interfacial tension numerically, we show that it controls the thread development, which can be described by an effective capillary number. Furthermore, we demonstrate that the applied methodology provide the means to measure the ultra-low but dynamically highly significant effective interfacial tension.