The effectiveness of operating an industrial UASB reactor, treating wastewater from the beer industry, with flows containing heavy metals was evaluated. A pilot-scale UASB reactor, already used to simulate the industrial reactor, was unsuccessfully employed. An easy start-up was obtained arranging it as an EGSB reactor. Considerations about this modification are reported. The effects of Cu(II), Ni(II) and Cr(III) ions on the anaerobic activity were analyzed by measurements of methane production rate and COD removal. The employed biomass was the sludge of the industrial UASB reactor, while a solution of ethanol and sodium acetate with COD of 3000 mg/L and a heavy metal concentration of 50 mg/L were continuously fed. Experimental results proved higher biomass sensitivity for copper and much slighter for nickel and chromium. Moreover, copper inhibition has been demonstrated to be less significant if a metal-free feed was provided to the system before copper addition.