The present study describes a case study on mango puree, in which focus is given to the effect of thermal processing (100–130 °C, 0–80 min) and high-pressure homogenisation (0–1300 bar) on the isomerisation of β-carotene. Both unit operations are of relevance for the production of mango puree. β-Carotene is an essential micronutrient which is present in a high amount in most mango cultivars, and it is important for human health due to its antioxidant and provitamin A capacity. It is known that these health-related properties of β-carotene are negatively affected by the conversion to cis-isomers. The results have shown that during high-pressure homogenisation of mango puree, β-carotene isomerisation was negligible. During thermal processing, on the other hand, an increase in β-carotene cis-isomer formation with increasing treatment intensity could be observed, although high temperatures and/or long treatment times were required to observe clear additional isomer formation. From a kinetic point of view, a fractional conversion model could be used to model the all-trans-β-carotene isomerisation in mango puree in the temperature and time range studied. In general, it can be concluded that a high percentage of β-carotene is present as cis-isomers in raw mango puree. Furthermore, only intense thermal processing of mango puree leads to the formation of additional cis-isomers in relevant amounts.