The usage of reclaimed wastewater (RWW) for irrigation of agricultural soils is increasingly being acknowledged for reducing water consumption by promoting reuse of treated wastewater, and for the delivery of extant nutrients in the soil. The downside is that RWW may be a vector for contamination of soils with contaminants of emerging concern (CECs), if left uncontrolled. Its usage is anticipated to alter the soil properties, consequently also the soil microbial community. In the present study, soil microcosms were set to monitor how short periods (up to fourteen days) of RWW irrigation influence the soil ecosystem, namely its physicochemical properties, functioning, and colonising microbiota (differentiating fungi from bacteria). Two scenarios were studied: clean soil and soil contaminated (spiked) with 9 CECs, at conditions that limit any abiotic decay processes, monitoring along time fluctuations in the taxonomic and functional microbiota diversity. As shortly as fourteen days, the irrigation of either soil with RWW did not significantly (p > 0.05) alter its physicochemical properties and scarcely impacted the bioremediation processes of the CECs that showed decay levels ranging from 24% to 100%. Bacillus spp. dominance was enhanced along time in all the soil microcosms (reaching over 70% of the total abundance on the 7th day) but the RWW help to preserve, to some extent, high bacterial diversity. Besides, irrigation with RWW acted as a buffer of the soil mycobiota, limiting alterations in its composition caused either along time (to a minor degree) or due to contamination with CECs (to a great degree). This includes limiting the rise of Rhizopus sp. relative abundance. Collectively, our data support the utility of short-term periods of RWW irrigation for preserving the soil microbial diversity and functioning, especially when fungi are considered.