We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15–25 °C or 20–30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community’s physiological profile and the bacterial community’s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20–30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome–invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.