The quinoxaline 1, possessing a 2,6-pyridyl-based amidothiourea moiety, with the view of forming a pre-organised molecular cleft, was developed as a fluorescent anion sensor. The sensing ability of 1 was evaluated in organic solution where both the ground and the excited state of 1 was affected upon recognition of anions such as acetate [as tetrabutylammonium salt (TBAAc) solution] at the amiodothiourea moieties in MeCN. The fluorescence of 1, with λmax at 477 nm, was, on all occasions quenched, upon anion recognition. Using TBAOH, we also show that the same anion-induced changes occurred; demonstrating that for this particular sensor, the anion-sensing takes place via a deprotonation mechanism. This anion-induced deprotonation event was further investigated by carrying out 1H NMR titrations on 1, using both AcO− and OH− in DMSO-d6.