Isoflurane is a frequently used anesthetic in small‐animal dissolution dynamic nuclear polarization‐magnetic resonance imaging (DNP‐MRI) studies. Although the literature suggests interactions with mitochondrial metabolism, the influence of the compound on cardiac metabolism has not been assessed systematically to date. In the present study, the impact of low versus high isoflurane concentration was examined in a crossover experiment in healthy rats. The results revealed that cardiac metabolism is modulated by isoflurane concentration, showing increased [1‐¹³C]lactate and reduced [¹³C]bicarbonate production during high isoflurane relative to low isoflurane dose [average differences: +16% [1‐¹³C]lactate/total myocardial carbon, –22% [¹³C]bicarbonate/total myocardial carbon; +51% [1‐¹³C]lactate/[¹³C]bicarbonate]. These findings emphasize that reproducible anesthesia is important when studying cardiac metabolism. As the depth of anesthesia is difficult to control in an experimental animal setting, careful study design is required to exclude confounding factors.