Summary (All‐E)‐ Lycopene undergoes geometrical isomerisation into (Z)‐lycopene isomers with thermal treatment. Influence of three isomerisation methods including ethyl acetate reflux, microwave‐assisted reflux and ultrasound/microwave‐assisted reflux, and isolation of (all‐E)‐lycopene from other carotenoids and (Z) lycopene isomers through selective inclusion by deoxycholic acid (3α, 12α dihydroxy‐5βcolan‐24‐oic‐acid, DCA) were investigated. The results showed that microwave and ultrasound/microwave‐assisted reflux were not significantly different at P < 0.05, but both were significantly different (P < 0.05) over refluxing in ethyl acetate, proportion of (Z)‐lycopene isomers reached 54% after refluxing for 5 h. Heterogeneous mixture of isomerised tomato oleoresin containing 54% (Z)‐lycopene isomers and 40% (all‐E)‐lycopene and deoxycholic acid in dichloromethane was incubated at 25 °C for 2 h. Then, the mixture was filtered and from the filtrate 96.6% (Z)‐isomers enriched lycopene was obtained. The processes can be used in the production of enriched (Z)‐lycopene isomers for food supplements and functional food industry as a natural bioactive ingredient.