CSE phenolic compounds, with proven anti-allergic activity, are thermolabile, prompting the need for investigation into alternative formulation and sterilisation methods when delivered in a beverage format. Cold plasma treatment holds potential for the sterilisation of beverages under milder conditions. This study investigated the stability of phenolic compounds from Cyclopia subternata extract (CSE) and its phytosomal formulation (CSE-P) in model beverage solutions subjected to thermal (70, 80, or 90 °C) and cold atmospheric pressure plasma jet treatments (CAPPJ) at different exposure times (0.5–2 min) and distances (2–6 cm). The effect of pH (3, 5 and 7) of the solutions was also investigated. Thermal treatments in water significantly degraded major phenolic compounds, mangiferin and 3′,5′-di-β-D-glucopyranosylphloretin (PDG); however, the CSE-P formulation improved their stability significantly. CAPPJ treatment in water (2 min at a 2 cm nozzle-to-product distance) had a minimal impact on phenolic stability in CSE and CSE-P. The pH of the solution affected phenolic degradation during thermal and CAPPJ treatment, with CSE-P exhibiting greater stability, particularly at pH 7 during heat treatment (e.g. 55 vs 72% decrease in PDG for CSE and CSE-P, respectively). Thermal treatment reduced the encapsulation efficiency and loading capacity of CSE-P at all pH levels (25–57%), but cold plasma only reduced these parameters at pH 7 (26%). This research demonstrated the potential of phytosomal technology to improve the stability of CSE phenolics. Cold plasma treatment showed promise as an alternative to traditional thermal methods for the sterilisation of phenolic-rich beverages.