High-speed counter-current chromatography (HSCCC) combined with HPLC were established to purify, for the first time, betacyanin isomers from Gomphrena globosa L. flowers. The mixture of tert-butyl methyl ether – butanol – methanol - water TBME-BuOH-MeOH-H2O (1.0% heptafluorobutyric acid HFBA) 2:2:1:5 (v/v/v/v) in reversed phase mode was used for preliminary purification of gomphrenin derivatives. Then, semiprep-HPLC was used to obtained ten pure betacyanins: gomphrenins II and III with their cis-isomers as well as sinapoyl-gomphrenin I and its corresponding diastereomers. This is the first study on separation of naturally coexisting acylated gomphrenin isomers. The isolated compounds showed a broad antimicrobial spectrum (in the range of 0.19–1.5 mg mL−1) by inhibiting the growth of all of food-borne pathogens tested. The antimicrobial activity of acylated betacyanins was higher than that of non-acylated gomphrenin I/isogomphrenin I. Therefore, the acylation with phenolic acids increases the activity of betacyanins against fungi and bacteria, suggesting a synergetic effect of the acylated moieties and the pigment chromophoric system on the activity, which was evaluated for the first time.