Herein, the particle size distributions (PSDs) and shape analysis of in vivo bioproduced particles from aqueous Au3+ and Eu3+ solutions by the cyanobacterium Anabaena sp. are examined in detail at the nanoscale. Generally, biosynthesis is affected by numerous parameters. Therefore, it is challenging to find the key set points for generating tailored nanoparticles (NPs). PSDs and shape analysis of the Au and Eu-NPs were performed with ImageJ using high-resolution transmission electron microscopy (HR-TEM) images. As the HR-TEM image analysis reflects only a fraction of the detected NPs within the cells, additional PSDs of the complete cell were performed to determine the NP count and to evaluate the different accuracies. Furthermore, local PSDs were carried out at five randomly selected locations within a single cell to identify local hotspots or agglomerations. The PSDs show that particle size depends mainly on contact time, while the particle shape is hardly affected. The particles formed are distributed quite evenly within the cells. HR-PSDs for Au-NPs show an average equivalent circular diameter (ECD) of 8.4 nm (24 h) and 7.2 nm (51 h). In contrast, Eu-NPs preferably exhibit an average ECD of 10.6 nm (10 h) and 12.3 nm (244 h). Au-NPs are classified predominantly as “very round” with an average reciprocal aspect ratio (RAR) of ~0.9 and a Feret major axis ratio (FMR) of ~1.17. Eu-NPs mainly belong to the “rounded” class with a smaller RAR of ~0.6 and a FMR of ~1.3. These results show that an increase in contact time is not accompanied by an average particle growth for Au-NPs, but by a doubling of the particle number. Anabaena sp. is capable of biosorbing and bioreducing dissolved Au3+ and Eu3+ ions from aqueous solutions, generating nano-sized Au and Eu particles, respectively. Therefore, it is a low-cost, non-toxic and effective candidate for a rapid recovery of these sought-after metals via the bioproduction of NPs with defined sizes and shapes, providing a high potential for scale-up.