Aerobic granular sludge is considered a promising technology for biological wastewater treatment, since it is more compact and resistant to shock and toxic loads than activated sludge systems. Furthermore, the monitoring of the aerobic granules structure, size and morphology has been growing in importance, proving to be suitable for operational and process control purposes. In this work, a sampling methodology is validated for the assessment of the ensemble granular and floccular biomass, by quantitative image analysis, in the presence of pharmaceutically active compounds, including 17β-estradiol and 17α-ethinylestradiol and the sulfamethoxazole. The employed sampling volumes were found to be adequate in obtaining a representative number of granules for all samples. Indeed, it was always obtained a variation lower than 5% in the average and standard deviation criterion of the main size, morphological and structural parameters. Moreover, it was also assessed the performance of the sieving process in successfully separating the granular and floccular biomass fractions and established a lower bound fraction size cut-off for the employed sieve. In addition, the continuity of the performed methodology and the image acquisition triplicates approach could also be validated. The ability of the proposed QIA procedure to monitor the studied AGS system was corroborated by the fact that 95% of the samples were able to be classified in the correct group (proof of concept).