Display omitted •Phycocyanin thermal instability limits its application as natural blue colourant.•Colour loss kinetics are affected by system composition (solute type, concentration).•At similar concentration, sucrose enhanced thermal stability more than trehalose.•The equivalent thermal effect did not discriminate the effect of disaccharide type.•Water activity play a key role on protein thermostability. The effect of heat and equivalent thermal effect (CTrefz) on discolouration of Spirulina algae extracts in water, sucrose and trehalose solutions at different concentration was investigated and kinetics of phycocyanin degradation evaluated by spectrophotometric and circular dichroism. At constant temperature, colour loss increased at increasing time and decreased at increasing solute concentration. Circular dichroism confirmed relation between colour loss and protein structure destabilization, and the thermostabilising effect of saccharides with sucrose performing better than trehalose. Apparent constant rate values determined by the Weibullian probabilistic model describe the corresponding phycocyanin degradation kinetics; a linear correlation between the activation energy and aw of the solutions has been found. Origin of phycocyanin and system saccharide concentration resulted significant discriminant factors on the discolouration when CTrefz was taken into account. Results may find application in product formulation and processing optimisation, thereby the use of Spirulina extracts as colouring foodstuff could be enhanced.