The mixotrophic green alga Chlamydomonas reinhardtii is able to grow photoautotrophically as well as uptake acetate as a carbon and energy source. The trophic regime strongly affects the growth rate and metabolism of the algae, what can have long-lasting aftermath even if the conditions have been changed. Mixotrophic pre-cultivation resulted in higher growth rate and physiological activity during the log phase in both mixotrophic and autotrophic cultures of C. reinhardtii. Metabolite profiling showed that acclimation has a pronounced effect on different aspects of primary metabolism, especially during the growth phase. These effects are partly explained by the legacy of previous trophic acclimation. Metabolic effects of acclimation were different in autotrophic and mixotrophic cultures. Common trends of mixotrophic acclimation consisted in higher levels of some carboxylates and amino acids. A pronounced effect of autotrophic acclimation was an increase in sugar accumulation. Also, changing conditions cause a metabolic perturbation expressed in variation of patterns of metabolite content over culture growth. The most stable patterns of dynamics were characteristics of free fatty acids and acylglycerols. Acclimation also affects the functional relationships between metabolite pools, which could be inferred from differences in correlation patterns. Finally, changes in trophic conditions triggered stronger correlations of metabolite content.