The use of microalgae in biological wastewater treatment has been widely studied. However, there is a dearth of information about estimating the microalgae and bacteria concentrations. In order to maintain a stable algal-bacterial system, it is necessary to quantify both the algal and bacterial biomasses. Typically, microalgae and bacteria from flocs in activated sludge contribute to better biomass settleability. However, flocs cause problems when it comes to estimating the individual biomass concentrations of microalgae and bacteria in a symbiotic algae-bacteria aggregate. This study aimed to find the best disintegration treatment with low influence on the viability of the microalgal cell determined by its photosynthetic activity. In the present work, biological (enzyme solution), chemical (formaldehyde), mechanical (glass bead-beating), and physical (sonication) treatments were performed on microalgae–bacteria flocs (ALBA flocs) to disintegrate the community as a pre-treatment step in order to develop a method for estimating the algal and bacterial concentration and to quantify the degree of disintegration. The effectiveness of the methods to disintegrate ALBA flocs in descending order are the following: sonication, bead-beating, formaldehyde and enzyme application. Sonication treatment (40 W, 6 min) showed the best disintegration performance of the microalgal-bacterial flocs, up to 90 % with 17 % loss of the algal photosynthetic activity. Bead-beating (3 mm diameter, 80 s) achieved 80 % of disintegration with only 6 % loss of its photosynthetic activity. These results demonstrate the possibility of mild disintegration of compact ALBA flocs without having any adverse impact on the microalgae cell. After these treatments, it becomes possible to estimate the individual biomass concentrations of algae and bacteria manually such as with a cell-counting chamber.