The stability of fructooligosaccharides (FOS) was investigated in yacon (Smallanthus sonchifolius Poepp. & Endl., Asteraceae) storage roots and blackcurrant-yacon juice mixtures. The roots and syrup are from yacon plants grown for NZ Biotechnologies, the only company in New Zealand licensed to grow yacon commercially for export. The hydrolysis of FOS in storage roots packaged in a semi-permable polymer was significantly reduced compared to unpackaged roots from the same plant, stored in the same conditions (5 °C for up to 72 days). The effectiveness of the packaging was dependent upon a complete seal around the root, indicating the need for selection of relatively straight and smooth roots for successful packaging. Blackcurrant-yacon juice mixtures offer the prebiotic effect of FOS combined with the antioxidant activity of blackcurrant juice. This study was designed to assess the effect of pasteurisation conditions on carbohydrate and polyphenol concentrations and antioxidant activity. The reduction in active ingredients per mL can then be compensated for by the initial formulation before pasteurisation. The rates of hydrolysis and release of FOS, 1-kestose, sucrose, D-glucose and D-fructose were calculated and agreed with previous studies with the exception of 1-kestose. The initial concentrations of polyphenols (330.67-524.4 gallic acid equivalent mg L⁻¹) and anthocyanins (1013.11-1362.25 cyanidin-3-glucoside equivalent mg L⁻¹) were also similar to other studies. The concentration of both polyphenols and anthocyanins decreased with heating time, but this difference was statistically significant at a 99.95 % confidence level only for anthocyanins. The decrease of anthocyanin concentration with time in blackcurrant-yacon juice without pH stabilisation was correlated with the rate of FOS hydrolysis. This indicates that the presence of FOS stabilizes the anthocyanins possibly by formation of a complex or compound. This is supported by evidence from elsewhere that dietary fibre-type molecules can transport antioxidants to the large bowel, with associated health effects.