Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between closely related aneuploid strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, as in other Eukaryotes, we observed attenuation of dosage effects for protein complex subunits and in addition, non-cytoplasmic proteins. Differentially expressed transcripts and proteins between aneuploid Leishmania strains also originated from non-aneuploid chromosomes. At protein level, these were enriched for proteins involved in protein metabolism, such as chaperones and chaperonins, peptidases, and heat-shock proteins. In conclusion, our results further support the view that aneuploidy in Leishmania can be adaptive. Additionally, we believe that the high karyotype diversity in vitro and absence of classical transcriptional regulation make Leishmania an attractive model to study processes of protein homeostasis in the context of aneuploidy and beyond. Author summary: Leishmania are protozoan parasites causing severe and stigmatizing diseases in humans and animals, worldwide. The parasites show several unique molecular features, one of them being an unusually high tolerance to aneuploidy, i.e. the presence of an abnormal number of chromosomes in the cell. While this is generally deleterious for higher Eukaryotes, this seems to be advantageous for Leishmania in certain conditions. However, the molecular and functional consequences of aneuploidy for the pathogen remained poorly understood. Here we studied the four main molecular layers of Eukaryotic cells: the genome, transcriptome, proteome, and metabolome. We present their first integrated analysis in aneuploid Leishmania. Our analyses show a strong impact of chromosome copy number on transcript- and protein abundance levels, ultimately correlating with the degree of observed metabolic differences. However, some specific proteins (subunits of protein-complexes and secreted proteins) encoded by aneuploid chromosomes showed reduced dosage effects. Reciprocally, we also found that some differential transcripts and proteins (chaperones, chaperonins and heat shock proteins) of aneuploid strains originated from non-aneuploid chromosomes. Our study provides new insights into mechanisms of molecular adaptation and regulation in Leishmania and the role of aneuploidy in this process. [ABSTRACT FROM AUTHOR]