The production of isolated metallic nanoparticles with multifunctionalized properties, such as size and shape, is crucial for biomedical, photocatalytic, and energy storage or remediation applications. This study investigates the initial particle formations of gold nanoparticles (AuNPs) bioproduced in the cyanobacteria Anabaena sp. using high-resolution transmission electron microscopy images for digital image analysis. The developed method enabled the discovery of cerium nanoparticles (CeNPs), which were biosynthesized in the cyanobacteria Calothrix desertica. The particle size distributions for AuNPs and CeNPs were analyzed. After 10 h, the average equivalent circular diameter for AuNPs was 4.8 nm, while for CeNPs, it was approximately 5.2 nm after 25 h. The initial shape of AuNPs was sub-round to round, while the shape of CeNPs was more roundish due to their amorphous structure and formation restricted to heterocysts. The local PSDs indicate that the maturation of AuNPs begins in the middle of vegetative cells and near the cell membrane, compared to the other regions of the cell.