A high-solid matrix of κ-carrageenan with polydextrose was developed to entrap α-linolenic acid, which is an omega-3 bioactive compound. Physicochemical analysis of this system utilised modulated DSC, dynamic oscillation in shear, ESEM, FTIR and WAX diffraction. The carbohydrate matrix was conditioned through an extensive temperature range to induce changes in molecular morphology and identify the network glass transition temperature. Thermally induced variation in phase morphology was employed to rationalise transportation patterns of the bioactive compound within the high-solid preparation. Thus, experimental observations using UV–vis spectroscopy modelled diffusion kinetics to document the mobility arresting effect of the vitrifying matrix on the micro-constituent. Within the glass transition region, results argue that free volume theory is the molecular process governing structural relaxation. Further, Less Fickian diffusion follows well the rate of molecular transport of α-linolenic acid as a function of time and temperature of observation in the condensed matrix.