•Side reactions produced serpentine and magnesium silicate hydroxide phases.•Extent of side reactions were elevated when experiments performed under nitrogen.•Side reactions reduced the magnesite yield by up to 40%.•Side reactions reduced the efficiency of direct aqueous carbonation process. This work discloses a possible explanation for the relatively low efficiency and yield observed in direct aqueous carbonation of heat activated serpentine which remained a critical unanswered question during three decades of ex-situ mineral carbonation research and development. The discovery of undesirable side reactions, occurring during direct aqueous carbonation of heat activated serpentine has been reported and investigated in detail. These reactions result in the reformation of crystalline serpentine and precipitation of amorphous magnesium silicate hydroxide phase/s on the surface of reacting feed particles. Reformation of serpentine occurs under relatively mild conditions (in terms of pressure and temperature) and after only a few minutes of reaction which is in stark contrast to the conditions and rates which occur during geological serpentinisation and other laboratory studies. Scanning Electron Microscopy and Energy Dispersive X-ray spectroscopy analyses showed precipitation of amorphous magnesium silicate hydroxide phase/s during carbonation process. Fourier Transform Infrared Spectroscopy and Thermogravimetric analyses identified and quantified free and hydrogen bonded hydroxyls of silanol groups in the structure of the reaction products when heat activated lizardite and antigorite were carbonated. The growth of a crystalline serpentine phase was confirmed and quantified by X-ray Diffraction and Thermogravimetric analyses in the reaction products when heat activated antigorite was used a feed.