We examined how the exposure to secondary stressors affected the functional and compositional responses of microbial communities along two metal pollution gradients in Polish forests and whether responses were influenced by the level of metal pollution. Basal respiration rate and community composition, as determined by 16S rRNA gene-based denaturing gradient analysis, were studied in laboratory-incubated microcosms, containing soil samples taken from different locations in the field gradients, and subjected to secondary stress factors (arsenic, salt, benzo[a]pyrene or flooding). Soils adapted to higher metal contamination levels were more resistant to arsenic and salt stress compared to less polluted soils, indicating that functional and compositional responses to these stresses were related to the level of historical pollution in the long-term contaminated forest soils. However, community composition and functioning in soils along the two gradients were resistant to benzo[a]pyrene and flooding stress. Changes in respiration were significantly related to changes in community composition. Knowledge on the functional gene capabilities prior to adding the secondary stressor benefitted understanding the functional responses toward additional stressors. Our study highlights that microbial communities selected for metal resistance in the field might also become more resistant against some secondary stress factors; however, the type of stress and the level of historical pollution play a decisive role in community-level responses toward secondary stressors.