Gas bubbles present a frequent challenge to the on-chip investigation and culture of biological cells and small organs. The presence of a single bubble can adversely impair biological function and often viability as it increases the wall shear stress in a liquid-perfused microchannel by at least one order of magnitude. We present a microfluidic strategy for in-plane trapping and removal of gas bubbles with volumes of 0.1–500 nL. The presented bubble trap is compatible with single-layer soft lithography and requires a footprint of less than ten square millimetres. Nitrogen bubbles were consistently removed at a rate of 0.14 μL min⁻¹. Experiments were complemented with analytical and numerical models to comprehensively characterize bubble removal for liquids with different wetting behaviour. Consistent long-term operation of the bubble trap was demonstrated by removing approximately 4000 bubbles during one day. In a case study, we successfully applied the bubble trap to the on-chip investigation of intact small blood vessels. Scalability of the design was demonstrated by realizing eight parallel traps at a total removal rate of 0.9 μL min⁻¹ (measured for nitrogen).