The PPA2/mitochondrial pyrophosphatase (inorganic pyrophosphatase 2) gene is localized to the long arm of chromosome number 4. The PPA2 protein, present in the mitochondrial matrix, is highly similar to members of the inorganic pyrophosphatase/PPase family. Inorganic pyrophosphatase catalyzes the hydrolysis of inorganic phosphate from diphosphates. Previous reports showed that within the sequence of the human PPA2 protein, amino acids 1-31 are the mitochondrial signal pre-peptide. Furthermore, Asp164, Asp169, and Asp201 are responsible for Mg2+ binding, Arg127 is critical for substrate binding, and Tyr138 serves as the proton donor site present in the active site of PPA2. This enzyme is essential for maintaining mitochondrial function and energy metabolism. Here, we identified the role of PPA2 in activating mitochondrial fission signaling. We found that PPA2 overexpression promotes mitochondrial fission by upregulating the mitochondrial translocation of phosphorylated DNM1L S616. Moreover, PPA2 interacts with MTFP1, a mitochondrial inner membrane protein, to induce fission signaling; cells knocked down for MTFP1 and overexpressing PPA2 failed to induce DNM1L activation and subsequent mitochondrial fission. Furthermore, in physiological conditions, PPA2 directed mitochondrial fission at the midzone through MFF-DNM1L, leading to mitochondrial proliferation. Interestingly, during mitochondrial stress following CCCP treatment, PPA2 triggers peripheral fission through FIS1 and DNM1L to segregate parts of damaged mitochondria, which is essential for mitophagy. In addition, PPA2 utilized the C-terminal LC3-interacting region (LIR) of MTFP1 for mitophagy-mediated clearance of damaged mitochondria. In conclusion, PPA2 activates mitochondrial fission signaling through MTFP1-DNM1L and is essential in defining the site of mitochondrial fission, leading to mitochondrial proliferation or mitophagy for maintaining mitochondrial homeostasis.