Two outdoor photobioreactors were operated to evaluate the effect of variable ambient temperature on an indigenous microalgae-nitrifying bacteria culture dominated by Chlorella. Four experiments were carried out in different seasons, maintaining the temperature-controlled PBR at around 25 ºC (by either heating or cooling), while the temperature in the non-temperature-controlled PBR was allowed to vary with the ambient conditions. Temperatures in the range of 15-30 ºC had no significant effect on the microalgae cultivation performance. However, when the temperature rose to 30-35 ºC microalgae viability was significantly reduced. Sudden temperature rises triggered AOB growth in the indigenous microalgae culture, which worsened microalgae performance, especially when AOB activity made the system ammonium-limited. Microalgae activity could be recovered after a short temperature peak over 30 ºC once the temperature dropped, but stopped when the temperature was maintained around 28-30 ºC for several days.