Phenotypic switching from tachyzoite to bradyzoite and vice versa is the fundamental mechanism underpinning the pathogenicity and adaptability of the protozoan parasite Toxoplasma gondii. Accumulation of cytoplasmic starch granules is a hallmark of the quiescent bradyzoite stage. The regulatory factors and mechanisms that contribute to amylopectin storage in bradyzoites remain incompletely known. Here, we show that T. gondii protein phosphatase 2A (PP2A) holoenzyme is composed of a catalytic subunit (PP2A-C), a structural subunit (PP2A-A) and a regulatory subunit (PP2A-B). Disruption of any of these subunits increased starch accumulation and disrupted the parasite differentiation. The putative PP2A holoenzyme substrates were identified by phosphoproteomics. PP2A contributes to the regulation of amylopectin metabolism via dephosphorylation of calcium-dependent protein kinase 2 at S679. Several putative PP2A substrates were found to play important roles in bradyzoite differentiation. Our findings establish PP2A as an integral component of the regulatory network mediating amylopectin metabolism and tachyzoite-bradyzoite transformation in T. gondii.