Phenolic compounds have been implicated as autotoxins of cucumber under mono-cropping management systems. Inhibition of cucumber growth may result from direct uptake of phenolic compounds or an indirect effect resulting from changes in soil microflora. In the present study we monitored the dynamics of soil phenolics in a continuously mono-cropped cucumber system and then assessed the effects of these compounds on soil microbial communities. Six phenolic compounds were identified in all soil samples in the continuously mono-cropping system. Soil total phenolic content increased extensively in the first cropping, but maintained a relatively stable level in the following croppings. Amendments of phenolics at the concentration detected in the soil showed inhibitory effects on cucumber seedling growth and stimulatory effects on soil dehydrogenase activity, soil microbial biomass carbon content and soil bacteria and fungi community sizes. Amendments of phenolics caused shifts in soil microbial community structures and soil bacteria and fungi communities had different responses. Our results suggested that direct phytotoxic effects of phenolics on cucumber probably did not happen in continuous mono-cropping systems, but they might indirectly influence cucumber performance by changing soil microbial communities.