Mitochondria generate ATP by creating a proton gradient across the inner membrane. This gradient also drives calcium uptake by the mitochondrial calcium uniporter (MCU) complex, while NCLX, encoded by SLC8B1, facilitates efflux. Mcu deficiency in various species does not result in obvious phenotypes, suggesting the existence of additional calcium transport systems. We here generated zebrafish lacking Tmbim5, a potential bidirectional mitochondrial calcium transporter, and Slc8b1, the probable NCLX ortholog. tmbim5 knockout fish exhibited impaired growth, muscle atrophy, increased brain cell death, and reduced mitochondrial membrane potential, but no significant changes in steady-state mitochondrial calcium levels. Slc8b1-deficient fish had increased larval mortality but were otherwise normal. Double knockouts of tmbim5/mcu and tmbim5/slc8b1 were viable with normal Mendelian distribution, indicating robust compensatory mechanisms maintain calcium homeostasis. tmbim5 knockout rescued the increased mortality in Slc8b1-deficient fish, and the NCLX inhibitor CGP-37157 lost its effect on behavior in Tmbim5-deficient but not Slc8b1-deficient zebrafish, implying shared, possibly antagonistic pathways. These findings suggest alternative pathways for mitochondrial calcium transport compensate for the loss of these proteins, enabling zebrafish survival.