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Propagation of a premixed flame from a closed to an open end in micro-channels with smooth non-slip isothermal walls is considered in the context of flame extinction dynamics. Powerful exponential flame acceleration in micro-channels with adiabatic walls has been demonstrated at the initial quasi-isobaric stage of the process [Bychkov et al., Phys. Rev. E 72, 046307 (2005)]. In contrast to the previous studies, here we investigate flame propagation in channels with isothermal walls. The problem is solved by means of high-fidelity laminar numerical simulations of the complete set of the Navier–Stokes combustion equations. For most of the problem parameter sets chosen, we obtain initial flame acceleration after ignition at the closed channel end. This acceleration resembles qualitatively the adiabatic case, but it develops noticeably slower, in an approximately linear regime instead of the exponential one and persists only for a limited time interval. Subsequently, heat loss to the walls reduces the temperature and hence the volume of the burnt gas behind the flame front, which produces a reverse flow in the direction of the closed channel end. When the amount of the burnt gas becomes sufficiently large, the reverse flow stops the acceleration process and drives the flame backwards with modifications of the flame front shape from convex to concave. Eventually, the flame extinguishes. Qualitatively, the process obtained reproduces a possible combustion failure during deflagration-to-detonation transition observed in previous experiments. We investigate the key characteristics of initial flame acceleration such as the acceleration rate and the maximum speed of the flame tip.