Yogurt is milk fermented product that becomes popular recently. In yogurt processing, fermenter is the main device. Lactobacillus sp. and Streptococcus sp. are two probiotic bacteria species that are common to be used in yogurt fermentation process. Both bacteria grow well in a specific range of temperature between 40-45 C, so temperature control in fermenter operational becomes one of the important things to ensure speed and quality of fermentation process. Fermentation process is a process with high degree of uncertainty and categorized as non-linear time invariant system. Thus, classical control system method is difficult to be implemented. To overcome this issue, intelligent control system can be implemented to yogurt's fermenter temperature control. One of intelligent control system method that can be implemented is fuzzy logic-based control system. In this study, fuzzy control system has been designed and implemented for fermenter temperature control. Control system algorithm is integrated in ATMega16 (for On-Off logic control) and ATMega32 (for Fuzzy Logic control) microcontrollers. Experimental results of fermenter control system shows that temperature profile of fermenter with fuzzy logic control system is more stable by settling time around an hour and 15 minutes and error average of -0.36 oC. Fermentation process for 16 hours with fuzzy logic controller produce yogurt with pH value of 3.66, total number of Lactobacillus sp. is 4.85 x 10 cfu/mL and Streptococcus sp. is 1.34 x 106 cfu/mL