(1) Background: The MultiPill-Exercise study was an exercise-based lifestyle intervention program for subjects with more than one lifestyle-related disease. Metabolomics-based approaches are an emerging tool in sports medicine, both in basic science and in clinical contexts. In this explorative, hypothesis-generating study, we aimed at defining metabolite patterns in subjects with multimorbidity and to test the predictive value of metabolite patterns for fitness adaptation. (2) Methods: A targeted tandem mass spectrometry (MS) approach on dried spots of capillary blood was employed, analyzing n = 86 subjects. (3) Results: In response to an acute bout of exhaustive exercise, aromatic amino acids (AA) tyrosine (Tyr) and phenylalanine (Phe), total carnitine (Cx) and short- as well as medium-chain acylcarnitines (SCA and MCA) were upregulated. Furthermore, concentrations of most metabolites were higher in males. Multiple regression defined free carnitine (C0), MCA and MCADelta, i.e. changes in concentrations during acute exercise, as important predictors of intervention-associated fitness adaptation after six months, explaining 24.8% and 24.4% of absolute and relative power gains associated with a respiratory quotient (RQ) of 1, a submaximal fitness parameter. (4) Conclusions: Our data suggest utility of metabolomics data in subjects with multimorbidity, both in the context of basic research and clinical applications.