MUSE is the next generation massive integral field spectrograph for the VLT, covering 1'x1' at a sampling of 0.2", and will begin operation in 2014. In return for the major effort in building this instrument, the MUSE consortium has been awarded 250 nights of VLT time for the guaranteed time observing. Due to the nature of MUSE data, each datacube obtained as part of the GTO programme will be used by most of the consortium nodes which are spread across Europe. Since the effort required in reducing the data is significant and to ensure uniformity in analysis, it was desirable to have a data management system that integrate data reduction, provenance tracking, quality control and data analysis. Here we present the MUSE-WISE system which incorporates these aspect. It is built on the Astro-WISE system originally designed to handle OmegaCAM imaging data. This has been extended to support 3D spectroscopic data, including quality control of the data. MUSE-WISE is currently used to handle simulated MUSE data, laboratory test data and we will report on our experience of this as well as discuss the central role of MUSE-WISE in the GTO phase and beyond.