We employ the yeast Saccharomyces cerevisiae as a model to study mechanisms of cellular aging in multicellular eukaryotes. Our high-throughput chemical genetic screen identified lithocholic bile acid (LCA) as a geroprotector which significantly slows yeast chronological aging. Using a combination of subcellular fractionation and mass spectrometry-based quantitative analyses, we revealed that exogenously added LCA enters yeast cells, is sorted to mitochondria, resides mainly in the inner mitochondrial membrane, and also associates with the outer mitochondrial membrane. We found that LCA elicits an age-related remodeling of phospholipid synthesis and movement within both mitochondrial membranes, thereby causing substantial changes in mitochondrial membrane lipidome and triggering major changes in mitochondrial size, number, and morphology. In synergy, these changes in the membrane lipidome and morphology of mitochondria alter the age-related chronology of mitochondrial respiration, membrane potential, ATP synthesis, and reactive oxygen species homeostasis. Our data revealed that the LCA-driven alterations in the age-related dynamics of these mitochondrial processes extend yeast longevity. Thus, mitochondrial membrane lipidome plays an essential role in defining yeast longevity. Using quantitative mass spectrometry, we demonstrated that LCA also alters the age-related dynamics of changes in levels of many mitochondrial proteins, as well as numerous proteins in cellular locations outside of mitochondria. These proteins belong to two regulons, each modulated by a different mitochondrial dysfunction. Proteins constituting these regulons 1) can be divided into several "clusters";, each of which denotes a distinct type of partial mitochondrial dysfunction that elicits a different signaling pathway mediated by a discrete set of transcription factors; 2) exhibit three different patterns of the age-related dynamics of changes in their cellular levels; and 3) are encoded by genes whose expression is regulated by the transcription factors Rtg1p/Rtg2p/Rtg3p, Sfp1p, Aft1p, Yap1p, Msn2p/Msn4p, Skn7p and Hog1p, each of which is essential for longevity extension by LCA. Our findings suggest that LCA-driven changes in mitochondrial lipidome alter mitochondrial proteome and functionality, thereby enabling mitochondria to operate as signaling organelles that orchestrate an establishment of an anti-aging transcriptional program for many longevity-defining nuclear genes. We propose a model for how such LCA-driven changes early and late in life of chronologically aging yeast cause a stepwise development of an anti-aging cellular pattern and its maintenance throughout lifespan.