Context. With two consecutive outbursts recorded in four months (October 2008 and January 2009), and a possible third outburst in 2007, 1E 1547.0-5408 is one of the most active transient anomalous X-ray pulsars known so far. Aims. Thanks to extensive X-ray observations, obtained both in the quiescent and active states, 1E 1547.0-5408 represents a very promising laboratory to gain insight into the outburst properties and magnetar emission mechanisms. Methods. We performed a detailed timing and spectral analysis of four Chandra, three INTEGRAL, and one XMM-Newton observations collected over a two week interval after the outburst onset in January 2009. Several Swift pointings, covering a 1.5 year interval, were also analyzed in order to monitor the decay of the X-ray flux. Results. We compare the characteristics of the two outbursts, as well as those of the active and quiescent states. We also discuss the long-term X-ray flux history of 1E 1547.0-5408 since its first detection in 1980, and show that the source displays three flux levels: low, intermediate and high.