We show that the low-temperature (5 K) emission spectrum of InSe nanoflakes, obtained by mechanical exfoliation of β-InSe, is characterized by unusual luminescence bands that are not present in the source material. These bands were observed both in the center and at the edges of the flakes, and their location at 30–70 meV below the expected position of the excitonic band bottom rules out intrinsic emission. In addition, the most intense luminescence band exhibits line narrowing and a pronounced blue shift of ~40 meV with the increase of excitation power from 40 to 1000 W/cm2. The shift is not observed in the low-temperature emission spectra of ultra thin (four monolayers) InSe flakes. Our data suggest that producing InSe flakes using mechanical exfoliation leads to the generation of optically active structural defects, presumably associated with a violation of the layer sequence and/or layer spacing inherent to β-InSe. The simplest type of these defects are bubbles and/or folds, the formation of which is accompanied by an increase in the distance between InSe layers and, as a consequence, produces repulsive (attractive) potential for electrons (holes). At low temperatures, these defects govern the luminescent properties of the flakes up to 6 monolayers by suppressing the intrinsic (exciton) emission. Some qualitative changes were observed only in ultrathin flakes with a thickness of ~4 monolayers. •Low-temperature luminescence of β-InSe nanoflakes has been studied.•Emission spectra of ultrathin InSe flakes have been obtained at 5K.•The impact of InSe exfoliation process on the intrinsic and defect-related emission has been demonstrated.