Trace-element anomalies in the continental crust (e.g., Nb-Ta-Pb) are useful to decipher the formation and evolution of continents. We found that the trace-element patterns of upper, middle, and lower crust are all marked by strongly negative phosphorus anomalies, which were not likely to have been generated directly by mantle melting. In order to address this “crust composition paradox,” we compiled major- and trace-element data from global arc magmas, igneous minerals, and deep arc cumulates and found that the phosphorus deficit in continental crust is coupled with an elevated Th/La ratio. This feature can be best explained by the fractional crystallization of apatite during arc magma evolution rather than the influence of a subducted slab. Accumulation of apatite-bearing mafic cumulates in deep arcs followed by foundering into the upper mantle causes the mismatch in the phosphorus systematics between the mantle and the continental crust. This process plays a critical role in shaping the chemical composition of continental crust.