The main objective of this research was to evaluate the effect of a 47 mT static magnetic field (SMF) applied at different times of the exponential growth phase of a Chlorella microalgae-bacteria consortium. For this, growth parameters, cell division, the photochemical activity of photosystem II (PS II), and the biochemical composition of the microorganisms were studied. Biomass concentration and productivity of cultures exposed to SMF increased concerning control cultures, reaching maximum values when this physical agent was applied in the early exponential phase, 0.89 g L−1 and 0.075 g L−1 d−1, respectively. In addition, SMF application stimulated binary and multiple cell division of cultures exposed during early and late exponential phases. PS II quantum yield was significantly increased over control cultures immediately after applying SMF during early (0.70) and late (0.73) exponential phases. In addition, in cultures exposed to SMF, the quantum yield for electron transport (ϕEo) increased, and the absorption flux per reaction center (ABS/RC) decreased, which was associated with an increase in the active reaction centers of PS II. Extracellular protein, carbohydrate, and polysaccharide content varied when SMF was applied during the early exponential phase. No significant differences were observed regarding the lipid content of the control cultures and those exposed to SMF. It is concluded that SMF increases the formation of radical pairs in photosystem II due to the increase in the number of active reaction centers, which could constitute the mechanism of action of this system.