Sirtuin 3 (SIRT3) is the main mitochondrial deacetylase and targets several crucial enzymes against oxidative stress. Recent reports suggest that SIRT3 could also participate in the quality and quantity control of mitochondria. The aim of this study was to analyze whether SIRT3 silencing in colon cancer cells could affect mitochondrial biogenesis and impair mitochondrial function. For this purpose, metastatic colon cancer cell line SW620 was transfected with a specific shRNA against SIRT3 to obtain a stable knockdown. Gene expression and protein levels of several proteins related to mitochondrial biogenesis and function were determined by RT-qPCR and Western blotting. Mitochondrial function was studied by analyzing COX, ATPase, and LDH enzymatic activities, oxygen consumption, superoxide levels, and mitochondrial membrane potential. Confocal images were also taken to study mitochondrial morphology, and cell motility and clonogenicity were also studied. SIRT3 silencing resulted in a reduced mitochondrial biogenesis and function, as evidenced by the decrease in proteins such as PGC-1α and mitochondrial transcription factor A and lower levels of OXPHOS complexes. Furthermore, COX activity and oxygen consumption were also diminished after SIRT3 knockdown. Finally, SIRT3-silenced cells showed mitochondrial aggregation compared with control cells as well as reduced motility and colony formation ability. In conclusion, SIRT3 silencing in SW620 cancer cells leads to decreased mitochondrial biogenesis and mitochondrial dysfunction, ultimately affecting cell viability and could be a therapeutic strategy to render cells more sensitive to treatment.