Perfluorinated substances (PFAS) are environmental pollutants that are difficult to break down chemically, thermally, or biologically. Due to its aqueous dispersibility, reactivity, high stability, flexibility, and economical synthesis, graphene oxide (GO) has been extensively researched in water purification. Adsorption is the most efficient and cost-efficient approach for PFAS removal from aqueous environments. Layered graphene-based materials have demonstrated a strong capacity for binding cationic ions and the capacity to build bridges between their deprotonated functional groups on the surface and anionic species like PFAS. In the present work, in situ powder diffraction data were collected as a function of time in temperature ramp up to 400 °C to explore the real-time evolution of the GO crystal structure before and after Ag functionalization and perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) loading. The PFOA and PFOS loading in the GO structure is mainly revealed by the (001) peak shift to greater 2θ values due to PFOA and PFOS interaction with GO interlayers and consequently decreasing of d-spacing distance. Around 150 °C, functional groups are expelled, structural defects are formed, and the (001, 2Θ≈10°) GO characteristic peak migrates. This is followed by a contraction that is accompanied by a reduction in d-spacing. At 350 °C, the reflection (001) disappears and the peak intensity of (002) increases, indicating that GO has been converted to reduced graphene oxide (rGO). The temperature at which PFOA and PFOS molecules degrade is between 375 and 400 °C, according to the GO-PFOA and GO-PFOS patterns. GO and AgGO samples underwent a partial but significant reduction at 400 °C. In the presence of silver, the dhkl values decrease (AgGO-PFOA, AgGO-PFOS < AgGO < GO-PFOA, GO-PFOS < GO). The above process found further confirmation when compared with the thermal analysis indicating that the thermal decomposition of GO and AgGO loaded with PFOA, PFOS is a multi-step reaction. Furthermore, differences in both shape and peak position for the DTA and DTG peaks also indicated that the thermal stability of PFOA was lower compared with PFOS. This information will help design an easy method based on graphene-Ag nanocomposites for removing hazardous perfluorinated contaminants from water and wastewater.