Biological reduction of soluble selenate to insoluble elemental selenium enables the removal and recovery of selenium from aqueous streams. Economic, efficient biological selenium recovery depends on properties of selenium particles such as size, density, stability, hydrophilic character and attachment to the biomass. In batch and fed-batch reactors using anaerobic sludge, the influence of pH (6-9) and temperature (20–50 °C) on the morphology, structure and stability of the biologically produced selenium particles were studied using SEM, XRD, and light microscopy. At a high pH or a high temperature these experiments resulted in grey crystalline hexagonal acicular selenium particles, while at a low pH combined with a low temperature red amorphous nanospheres were dominant. Particle stability tests were carried out by changing the temperature or pH after the particles had formed. Red amorphous selenium spheres (produced at pH = 7 and 30 °C) transformed gradually towards the grey hexagonal structure at 50 °C over a period of three weeks, whereas the transformation was less or not detected under other process conditions (according XRD). We show here that biological selenium particle crystallinity, shape and color can be controlled by temperature and pH. However, the choice for the temperature and pH in the bioreactor should not limit the biomass' reduction capacity of selenate. The production of crystalline particles is an important first step to grow larger selenium particles in the future in order to reduce costs for selenium recovery in bioreactors.