This work aimed to evaluate the hydrogen production rate (HPR) from lactate using the acidic fermented cheese whey (FCW) substrate, focusing on the lactate and lactate–acetate pathways. The lactate pathway was evaluated in three stages. In the first stage, the reactor was fed with cheese whey (CW; phase I) and then with FCW to phases II and III. Two hydraulic retention times (HRT) were tested in the second stage: 6 and 4.5 h. In the third stage, four pH levels were evaluated: 6, 5.5, 5, and 4.5 (reaching 1.2 L H2/L·d). The lactate-acetate pathway was first assessed in batch test, observing an enhancement of the HPR using FCW-acetic acid (HAc) at a ratio of 8.25. The continuous operation at this ratio reached 3.2 L H2/L·d. The relationship between Clostridium, high HPR, and lactate removal was positively correlated at a pH of 5 and HRT of 4.5 h.