Metals play a crucial role in cellular biology. Bulk and trace metals such as calcium and manganese regulate a plethora of cellular processes ranging from signaling and oxidative stress to proteostasis and energy metabolism. Fine-tuning metal levels and distribution safeguards all forms of life from compromised cellular fitness and cell death elicited by metal deficiency or overload. However, the underlying molecular mechanisms eventually leading to cellular demise remain elusive. In this thesis, we studied the fundamental impact of disrupted metal homeostasis on cellular survival focusing on mitochondrial and lysosomal processes in Saccharomyces cerevisiae and Drosophila melanogaster. In Paper I, we establish Coenzyme Q (CoQ) biosynthesis in mitochondria as the prime target of cellular manganese overload and propose a molecular mechanism underlying manganese toxicity. Combining proteomics, genome-wide screening and comprehensive metal analyses, we identify mismetallation of the di-iron hydroxylase Coq7, an enzyme of CoQ biosynthesis, as cause for the CoQ deficiency upon manganese overload. Overexpression of Coq7 not only restored CoQ-mediated electron transport through the respiratory chain but also prevented age-associated death. Expanding from trace to bulk metals, we further assessed the impact of disrupted calcium and manganese homeostasis on cellular survival. In Paper II, we created a fluorescence-based reporter system for the Ca²⁺/calmodulin-dependent phosphatase calcineurin, a nexus for cell stress-induced signaling. Combining our reporters with a live/dead staining allows for quantification of acute and chronic changes in calcium signaling in living, unperturbed cells. In Paper III, we elucidate the impact of nutritional regimes known to improve cellular survival on cells compromised in the handling of calcium and manganese due to the absence of Pmr1, a Ca²⁺/Mn²⁺ ATPase of the secretory pathway. We demonstrate that caloric restriction prevents manganese-induced disruption of mitochondrial energy metabolism and improves survival independent of calcineurin activity and CoQ biosynthesis. In Papers IV and V, we studied the interplay of metal levels and calcium signaling in the context of neurodegeneration and report that calcineurin stimulates lysosomal proteolysis, thereby preventing proteotoxicity in yeast and Drosophila models for Parkinson’s disease. Collectively, our results provide new insights into the consequences of disrupted metal homeostasis for cellular fitness and unravel a novel link between manganese overload, mitochondrial bioenergetics and CoQ biosynthesis conserved across species.