The expansion of agriculture and the need for sustainable practices drive breeders to develop plant cultivars adapted to abiotic stress, including nutrient deficiency. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two inbred popcorn lines, L80 (P-inefficient) and P7 (P-efficient), to low and high P availability. Physiological measurements, proteomics, and metabolomics were employed to unravel the metabolic pathways and compounds associated with efficient phosphorus utilization in P7. We observed significant differences in protein abundance between P supply conditions and the two inbred lines. A total of 421 differentially accumulated proteins (DAPs) were identified in L80, while 436 DAPs were found in P7. These proteins were involved in photosynthesis, protein biosynthesis, the production of secondary metabolites, and energy metabolism. Notably, the flavonoids apigenin, luteolin, and naringenin were found to accumulate more in P7, along with phenolic acids such as syringic acid, cinnamic acid, and gallic acid. Conversely, the P-inefficient line exhibited higher accumulation of phytohormones like indole-3-acetic acid, gibberellin A1, methyl IAA, abscisic acid, and 12-oxophytodienoic acid. Our results allow us to understand the major differences in the P-deficiency response mechanisms between P7 and L80 and provide new insights into the mechanisms needing investigation to improve use of P in popcorn.