Updated project metadata. The intracellular parasite Toxoplasma gondii resides within a membrane bound parasitophorous vacuole and secretes an array of proteins to establish this replicative niche during acute stage of infection. When rapidly dividing tachyzoites convert to chronic stage bradyzoites, many secreted proteins are reported to dynamically redistribute as the cyst forms and secreted kinases are known to play a role in cyst formation. Using quantitative phosphoproteome and proteome analysis comparing tachyzoite and bradyzoite stages, we reveal widespread differential phosphorylation of secreted proteins. These data support a model in which secreted kinases and phosphatases are important to dynamically regulate parasite secreted proteins during stage conversion.