The overall aim of the present study was to explore the relationship between medicinal use and fatty fish consumption on heart rate variability (HRV) and heart rate (HR) in a group of forensic inpatients on a variety of medications. A total of 49 forensic inpatients, randomly assigned to a fish group (n = 27) or a control group (n = 22) were included in the present study. Before and by the end of the food intervention period HR and HRV were measured during an experimental test procedure. An additional aim of this paper is to show how multivariate data analysis can highlight differences and similarities between the groups, thus being a valuable addition to traditional statistical hypothesis testing. The results indicate that fish consumption may have a positive effect on both HR and HRV regardless of medication, but that the influence of medication is strong enough to mask the true effect of fish consumption. Without correcting for medication, the fish group and control group become indistinguishable (p = 0.0794, Cohen’s d = 0.60). The effect of medication is demonstrated by establishing a multivariate regression model that estimates HR and HRV in a recovery phase based on HR and HRV data recorded during psychological tests. The model performance is excellent for HR data, but yields poor results for HRV when employed on participants undergoing the more severe medical treatments. This indicates that the HRV behavior of this group is very different from that of the participants on no or lower level of medication. When focusing on the participants on a constant medication regime, a substantial improvement in HRV and HR for the fish group compared to the control group is indicated by a principal component analysis and t-tests (p = 0.00029, Cohen’s d = 2.72). In a group of psychiatric inpatients characterized by severe mental health problems consuming different kinds of medication, the fish diet improved HR and HRV, indices of both emotional regulation and physical health.