Our previous studies have shown that glycerol fermentation by H. alvei AD27 strain was accompanied by formation of high quantities of lactate (LA). The ultimate aim of this work was elimination of excessive LA production in the 1,3-PD producer cultures. Group II intron-mediated deletion of ldh (lactate dehydrogenase) gene in an environmental isolate H. alvei AD27 strain has been conducted. The effect of the Δldh genotype in H. alvei AD27 strain varied depending on the culture medium applied. Under lower initial glycerol concentration (20 g/L), LA and 1,3-PD production has been fully abolished, and the main carbon flux was directed to ethanol (EtOH) synthesis. On the other hand, at higher initial glycerol concentrations (40 g/L), 1,3-PD and LA production was recovered in the recombinant strain. The final titer of 1,3-PD and EtOH were corresponding for the recombinant and the WT strains, respectively, while the Δldh genotype was expressed by significantly decreased LA titer. The by-products profile was altered upon ldh gene deletion, while glycerol utilization and biomass accumulation remained unaltered. As indicated by flow-cytometry analyses, the internal pH was not different for the WT and the recombinant Δldh strains over the culture duration, however, the WT strain was characterized by higher redox potential.