Observations of Archean organic-walled microfossils suggest that their fossilization took place through both encapsulation and permineralization. In this study, we investigated microfossils from the ca. 3.0 Ga Farrel Quartzite (Pilbara, Western Australia) using transmitted light microscopy, scanning electron microscopy, Raman microspectrometry, and nanoscale secondary ion mass spectrometry (NanoSIMS) ion microprobe analyses. In contrast to previous studies, we demonstrated that permineralized microfossils were not characterized by the micrometric spatial relationships between Si and C-N as observed in thin sections. Permineralized microfossils are composed of carbonaceous globules that did not survive the acid treatment, whereas encapsulated microfossils were characterized due to their resistance to the acid maceration procedure. We also investigated the microscale relationship between the 12C14N- and 12C2- ion emission as a proxy of the N/C atomic ratio in both permineralized and encapsulated microfossils. After considering any potential matrix and microtopography effects, we demonstrate that the encapsulated microfossils exhibit the highest level of geochemical preservation. This finding shows that the chemical heterogeneity of the microfossils, observed at a spatial resolution of a few hundreds of micrometers, can be related to fossilization processes. Key Words: Carbonaceous matter-Farrel Quartzite-Fossilization-NanoSIMS-Nitrogen-Permineralization. Astrobiology 17, 1192-1202.