Heat-induced changes in aspalathin, iso-orientin, and orientin content of ready-to-drink (RTD) green rooibos iced tea formulations were investigated. An organic-solvent-based aspalathin-enriched extract prepared from green rooibos was used "as-is" or encapsulated with ascorbic acid in a water-soluble nanomicelle-based carrier system. The common iced tea ingredients, ascorbic acid, and/or citric acid were added to the iced tea containing green rooibos extract. Only citric acid was added to the iced tea containing the nanomicelles. Heat treatments consisted of pasteurization (93 °C/5 min and 93 °C/30 min), normal-temperature sterilization (NTS; 121 °C/15 min), and high-temperature sterilization (HTS; 135 °C/4 min). Pasteurization had little or no effect on the flavonoid content. NTS and HTS induced significant losses in the flavonoids. The addition of citric and ascorbic acids improved the stability of the flavonoids, but encapsulation of green rooibos extract with ascorbic acid in nanomicelles did not offer additional stability. The only benefit of using the water-soluble nanomicelles was the improved clarity of the RTD product. Iso-orientin and orientin contents were substantially less affected than aspalathin by the heat treatments, partially because of conversion of aspalathin to these flavones, which countered losses. 5-Hydroxymethylfurfural (HMF), a known dehydration product of hexoses under mild acidic conditions and also a degradation product of ascorbic acid, was observed in formulations containing citric and/or ascorbic acids.