Type 2 diabetes mellitus (T2DM) is frequently accompanied by affective disorders with a prevalence of comorbid depression of around 25%. Nevertheless, the biomarkers of affective symptoms including depression and anxiety due to T2DM are not well established. The present study delineated the effects of serum levels of copper, zinc, β-arrestin-1, FBXW7, lactosylceramide (LacCer), serotonin, calcium, magnesium on severity of depression and anxiety in 58 men with T2DM and 30 healthy male controls beyond the effects of insulin resistance (IR) and atherogenicity. Severity of affective symptoms was assessed using the Hamilton Depression and Anxiety rating scales. We found that 61.7% of the variance in affective symptoms was explained by the multivariate regression on copper, β-arrestin-1, calcium, and IR coupled with atherogenicity. Copper and LacCer (positive) and calcium and BXW7 (inverse) had significant specific indirect effects on affective symptoms, which were mediated by IR and atherogenicity. Copper, β-arrestin-1, and calcium were associated with affective symptoms above and beyond the effects of IR and atherogenicity. T2DM and affective symptoms share common pathways, namely increased atherogenicity, IR, copper, and β-arrestin-1, and lowered calcium, whereas copper, β-arrestin-1, calcium, LacCer, and FBXW7 may modulate depression and anxiety symptoms by affecting T2DM.