In vivo molecular imaging tools are crucially important for elucidating how cells traffic through complex biological systems. Toward this goal, a new approach was recently developed to track the migration of live single cells in vivo using whole-body positron emission tomography (PET). Here, we report several innovations for enhancing the performance and utility of this methodology. First, we streamlined the cell radiolabeling workflow, using 18F-fluorodeoxyglucose (FDG) as the label and an automated microfluidics device for dispensing single cells. This highly reproducible approach could label cells with upwards of 100 Bq/cell while maintaining viability, enabling simultaneous PET imaging of multiple single cells in the same subject with unprecedented contrast. Second, we leveraged the performance of a high-sensitivity, low-background PET scanner and a custom tracking algorithm (PEPT-EM) to push the cellular detection limit to below 4 Bq/cell, enabling in vivo PET acquisitions as short as 1 minute and tracking of low-radioactivity cells. Finally, as a proof of concept, we tracked the distribution and fate of over 70 melanoma cells after intracardiac injection and found that they primarily arrested in the small capillaries of the pulmonary, musculoskeletal, and digestive organ systems. In conclusion, this study supports the emerging potential of PET for tracking single cells at the whole-body level, providing unmatched sensitivity and insights into the earliest phases of cell trafficking during physiological and pathological processes and cell-based therapies.