Hydrogen production is a viable alternative for the valorization of agro-industrial effluents, such as winery wastewater (WW). One limitation of using new substrates is system stability, where high organic loading rates favor high productivities. Using a new reactor configuration of packed bed reactors, different biomass purge strategies were evaluated in parallel reactors to maintain the stability in the long-term feeding WW, along with a community evaluation. A frequently programmed purge of biofilm and suspended biomass (every 7–8 days) resulted in the most stable hydrogen productivity, 930 mL H2 L−1d−1, unlike only purging biofilm or not programing the purge (<650H2 L−1d−1). The long-term stability is explained by a proper balance of the microbial genera in the reactor, Lactobacillus, Pectinatus, and Clostridium. This work proposes an innovative reactor configuration and operation strategy using WW, where a programmed biomass purge helps control the lactate and hydrogen-producing microbial groups.