Phosphorus is an essential limited nutrient for plant growth and modern agricultural productivity. A comprehensive understanding of how plants respond to phosphate starvation is essential to develop more phosphate-use efficient crops. Here we quantified protein-level responses to phosphate (PO4-) and phosphite (PO3-) in Arabidopsis thaliana suspension cells, relative to a phosphate-starved state using label-free proteomics and phosphoproteomics. Phosphite is similarly sensed and taken up by plants as phosphate but cannot be used as a source of phosphorus. Phosphite is hence a useful tool to delineate between non-specific processes related to sensing and transport, and specific responses to phosphorus nutrition. We find that responses to phosphate and phosphite occur mainly at the level of protein phosphorylation, complemented by limited changes in protein abundance, primarily in protein translation, and phosphate transport and scavenging proteins. Phosphorylation changes in proteins involved in core processes such as translation, RNA splicing and kinase signalling are especially important in phosphate starvation. We also find differential phosphorylation in response to phosphate and phosphite in 69 proteins, including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 histone acetyltransferase—potential phospho-switches sensing changes in phosphorus nutrition. Our study hence illuminates several new aspects of the phosphate-starvation response and identifies important targets for further investigation and crop improvement.