Phosphorus (P) assimilation and polyphosphate (polyP) synthesis were investigated in Chlamydomonas reinhardtii by supplying phosphate (PO43−; 10 mg P·L−1) to P‐depleted cultures of wildtypes, mutants with defects in genes involved in the vacuolar transporter chaperone (VTC) complex, and VTC‐complemented strains. Wildtype C. reinhardtii assimilated PO43− and stored polyP within minutes of adding PO43− to cultures that were P‐deprived, demonstrating that these cells were metabolically primed to assimilate and store PO43−. In contrast, vtc1 and vtc4 mutant lines assayed under the same conditions never accumulated polyP, and PO43− assimilation was considerably decreased in comparison with the wildtypes. In addition, to confirm the bioinformatics inferences and previous experimental work that the VTC complex of C. reinhardtii has a polyP polymerase function, these results evidence the influence of polyP synthesis on PO43− assimilation in C. reinhardtii. RNA‐sequencing was carried out on C. reinhardtii cells that were either P‐depleted (control) or supplied with PO43− following P depletion (treatment) in order to identify changes in the levels of mRNAs correlated with the P status of the cells. This analysis showed that the levels of VTC1 and VTC4 transcripts were strongly reduced at 5 and 24 h after the addition of PO43− to the cells, although polyP granules were continuously synthesized during this 24 h period. These results suggest that the VTC complex remains active for at least 24 h after supplying the cells with PO43−. Further bioassays and sequence analyses suggest that inositol phosphates may control polyP synthesis via binding to the VTC SPX domain.