Dopamine is an essential neurotransmitter involved in multiple physiological functions, and altered dopamine levels are implicated in several neurological and psychiatric disorders. A novel technique to functionalize quartz nanopipettes with ca. 10 nm orifice with molecular recognition elements named aptamers is proposed. The dopamine-specific aptamers undergo conformational reorganization upon target binding and recognize dopamine with high specificity and selectivity. Multiple dopamine detection in flow are demonstrated thanks to the reset-ability of aptamers. Furthermore, the specific binding is examined through complementary surface sensitive techniques, such as quartz crystal microbalance with dissipation and optical waveguide lightmode spectroscopy. In addition, double pore nanopipettes were functionalized with the dopamine aptamer and the control sequence to perform multiplexed measurements within confined spaces.