Toxoplasma gondii is an obligate intracellular parasite capable of invading any nucleated cell. Three main clonal lineages (type I, II, III) exist and murine models have driven the understanding of general and strain-specific immune mechanisms underlying Toxoplasma infection. However, murine models are limited for studying parasite-leukocyte interactions in vivo, and discrepancies exist between cellular immune responses observed in mouse versus human cells. Here, we develop a zebrafish infection model to study the innate immune response to Toxoplasma in vivo. By infecting the zebrafish hindbrain ventricle, and using high-resolution microscopy techniques coupled with computer vision driven automated image analysis, we reveal that Toxoplasma invades and replicates inside a parasitophorous vacuole to which type I and III parasites recruit host cell mitochondria. We show that type II and III strains maintain a higher infectious burden than type I strains. To understand how parasites are being cleared in vivo, we analyzed Toxoplasma-macrophage interactions using time-lapse and correlative light and electron microscopy. Strikingly, macrophages are recruited to the infection site and play a key role in Toxoplasma control. These results highlight in vivo control of Toxoplasma by macrophages, and illuminate the possibility to exploit zebrafish for discoveries within the field of parasite immunity.