Craft beers manufactured by small local breweries are becoming increasingly popular throughout the world due to their unique composition, taste and flavor. However, the ingredients used in brewing might lead to thermal processing contaminants in the final product. Thus, the aim of this study was to evaluate the levels of acrylamide (AA), polycyclic aromatic hydrocarbons (PAHs) and 3-monochloropropane-1,2-diol (3-MCPD) in dark craft beers available in Poland and the Czech Republic. The samples were prepared using a modified QuEChERS method that had been optimized and validated in-house; they were then analyzed by gas chromatography-mass spectrometry (GC–MS) and high-performance liquid chromatography with a diode array detector (HPLC-DAD). The results showed that PAHs were found in most of the analyzed beer samples. The total sum of PAHs ranged from 6.43 to 26.93 μg kg−1; the highest level of PAH4 content was 2.79 μg kg−1. Only three beer samples were free of any heavy PAHs. 3-MCPD and AA were also detected in all the beers, reaching levels of 14.0 μg kg−1 and 363 μg kg−1, respectively. The levels of 3-MCPD and AA were significantly higher in Polish beers than in beers from the Czech Republic. Higher amounts of 3-MCPD were found in beers containing roasted malt. A risk assessment was conducted for 3-MCPD and PAHs; it indicated that consumption of the examined beer samples should not cause any risk to human health. However, due to the high levels of acrylamide, regular consumption of dark beers poses a serious threat to human health and therefore should be strictly limited.