Abstract BACKGROUND Microalgal biofilm systems are a promising approach for wastewater treatment and for production of biodiesel precursors through simple biomass harvesting. However, the low concentration of nutrients in wastewater limits possible approaches for microalgal growth. The effective decoupling of the solid retention time (SRT) and the hydraulic retention time (HRT) in biofilm reactors as an alternative for increasing microalgae growth and biodiesel performance in low‐strength wastewater has not been investigated. In this study, we tracked how decoupling the SRT and the HRT influences the removal of organics and nutrients, the biomass productivity and the production of fatty acid methyl esters (FAME). RESULTS Three perturbations of the HRT, SRT and liquid level (LL) with regards to the base case condition (HRT 2.6 h; SRT 21 days, LL 5 mm) performance were analyzed. The base case showed the highest TN and TP removal (>50%) outcomes with high pH values (>10). A decrease of HRT and SRT from 2.6 to 1.3 h and 21 to 10 days, respectively, promoted an increment of microalgal productivity ≤5.8 ± 0.7 g m −2 day −1 . A short HRT of 1.3 h enhanced the nitrogen removal rate up to 1.2 g N m −2 day −1 , which triggered an increase in the FAME productivity and microalgal density on the biofilms without affecting their productivity. CONCLUSION Our study demonstrated that the strategy of decoupling HRT and SRT allows operation at shorter HRTs, promoting microalgal growth without affecting FAME production in low‐strength municipal wastewater. © 2023 Society of Chemical Industry (SCI).