Abstract Magnetar giant flares are rare and highly energetic phenomena observed in the transient sky whose emission mechanisms are still not fully understood. Depending on the nature of the excited modes of the magnetar, they are also expected to emit gravitational waves (GWs), which may bring unique information about the dynamics of the excitation. A few magnetar giant flares have been proposed to be associated with short gamma-ray bursts. In this paper we use a new gravitational-wave search algorithm to revisit the possible emission of GWs from four magnetar giant flares within 5 Mpc. While no gravitational-wave signals were observed, we discuss the future prospects of detecting signals with more sensitive gravitational-wave detectors. In particular, we show that galactic magnetar giant flares that emit at least 1% of their electromagnetic energy as GWs could be detected during the planned observing run of the LIGO and Virgo detectors at design sensitivity, with even better prospects for third-generation detectors.