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Metal-based flocculants are commonly used for biomass harvesting in microalgae-based bio-refineries. Besides the high separation efficiency, additional aspects should be considered, related to the toxicity of metals for the algal biomass. Partitioning tests for commonly used flocculants (i.e., FeCl3 and Al2(SO4)3) showed that metals were mostly transferred to the solid phase with more than 95% of dosed metal ending up into the biomass, and low metal concentrations in the liquid effluent (lower than 0.4 mg L−1 for both metals), thus allowing for water reuse. Photosynthesis inhibition was tested on microalgae and microalgae-bacteria cultures, using a standardized photo-respirometry protocol in which typical concentrations used during coagulation-flocculation were assessed. Modelling dose-response curves, concentrations corresponding to 50% inhibition (IC50) were obtained, describing short-term effects. The obtained IC50 ranged from 13.7 to 28.3 mg Al L−1 for Al, and from 127.9 to 195.8 mg Fe L−1 for Fe, showing a higher toxicity for the Al-based flocculant. The recovery of photosynthesis inhibition was also quantified, to evaluate the possibility of reusing/recycling the harvested biomass. The results highlighted that the residual photosynthetic activities, evaluated after 1 h and 24 h of exposure to metals were partially recovered, especially for Al, passing from 67.3% to 94.6% activity, respectively, while long-term Fe effects were stronger (passing from 64.9% to 77.6% activity). A non-toxic flocculant (cationic starch) was finally tested, excluding potential effects due to biomass aggregation, as the reduction of photosynthetic activity only reached 3.4%, compared to control. Relevant modifications to the light availability and the optical properties of algal suspensions were assessed, identifying a strong effect of iron which caused an increase of the light absorbance up to approximately 40% at high Fe concentrations. Possible implications of dosing metallic flocculants in MBWWT processes are discussed, and suggestions are given to perform inhibition tests on flocculating chemicals.