The average and the local structure of phosphorus-treated HZSM-5 zeolites were investigated by means of atom probe tomography, powder X-ray diffraction (at ambient and cryogenic temperatures) and 1H, 29Si, 27Al, and 31P magic angle spinning (MAS) solid state nuclear magnetic resonance (NMR) spectroscopy. Phosphatation to yield a product with P/Al ≤ 1 followed by thermal treatment leads to breaking of the Si-OH-Al bridging groups, and subsequent partial dealumination of the zeolite framework, as shown by the contraction of the orthorhombic unit-cell volume and by the loss of tetrahedral framework Al, as observed in the 27Al Multiple Quantum (MQ) MAS NMR spectrum. Most of the framework Al is present in an electronic environment distorted by the presence of phosphorus and appears not to be involved in classic Si-OH-Al Brønsted acid sites. The 31P MAS NMR signals indicate that phosphorus interacts with the zeolitic framework to locally form silico-aluminophosphate (SAPO) domains and the presence of a new kind of acidic site was confirmed by the resonance at ∼8.6 ppm in the 1H MAS NMR spectra, attributed to P-OH groups. Increasing the phosphorus loading (P/Al ≫ 1) promotes further dealumination of the framework and cross-dehydroxylation between P-OH and Si-OH species, leading to the formation of a crystalline silicon orthophosphate phase. With decreasing Al content, the monoclinic HZSM-5 structure becomes preferred, especially at 85 K where the strain relaxation is higher. However, the presence of a higher amount of silicophosphate impurities hinders the low-temperature strain release of the framework, indicating that some of these species are localized in the zeolite pores and contribute to the strain build up.