Giardia lamblia is a protistan parasite causing acute and chronic diarrheal disease in over one billion people worldwide, primarily in areas lacking adequate water treatment. Animal hosts ingest Giardia cysts that excyst in the gut to become motile trophozoites. Trophozoites colonize the small intestine, later differentiating into infectious cysts that are excreted and can contaminate water sources. Due to the limited accessibility of the gastrointestinal tract, our understanding of in vivo temporal and spatial dynamics of giardiasis is largely inferred from parasite physiology in laboratory culture. While in vitro models of giardiasis are informative, they may not adequately mirror in vivo parasite physiology in the host. To evaluate in vivo giardiasis directly, we developed bioluminescent imaging (BLI) methods to quantify temporal and spatial dynamics of giardiasis in mice using parasites expressing constitutive or encystation-specific luciferase bioreporters. Consistent with prior work, BLI confirms that metabolically active parasites primarily colonize the proximal small intestine. Contrasting with previous studies, we find that encystation is initiated and peaks early during infection and is localized to foci of high parasite density in the small intestine. Both BLI and immunostaining of encystation-specific vesicles (ESVs) corroborate that encystation is initiated in the proximal rather than the distal small intestine. This non-invasive method of imaging giardiasis provides an unprecedented and precise quantification of in vivo temporal and spatial patterns of infection, and an improved animal model for evaluation of anti-giardial drugs.