Acidified soils in greenhouse vegetable systems constrain crop production and soil ecological functions. This study investigated the effects of different amendment treatments on soil ecological factors in acidified soils under greenhouse spinach cultivation in Baoqing County, China. Three treatments were established: farmyard manure alone (T1), Haijuneng soil amendment, an alkaline oyster-shell-based soil conditioner, alone (T2), and the combined application of farmyard manure and Haijuneng soil amendment (T3). High-throughput sequencing of the 16S rRNA gene combined with functional prediction was used to analyze soil bacterial community characteristics and their relationships with soil physicochemical properties and enzyme activities. The results showed that soil pH increased significantly under T2 compared with T1 (4.59 vs. 4.14), along with higher exchangeable calcium (16.11 vs. 12.20 cmol kg⁻¹) and exchangeable magnesium (5.54 vs. 3.83 cmol kg⁻¹). In contrast, T3 showed the highest organic matter content (48.54 g kg⁻¹) and phosphatase activity. Compared with T1, both T2 and T3 increased urease activity and altered bacterial community structure and functional composition, while microbial diversity was highest under T2. Soil pH and available phosphorus were the main factors driving bacterial community variation, whereas pH, exchangeable calcium, and exchangeable magnesium were significantly correlated with multiple dominant genera and KEGG level 2 pathways. Overall, the amendment strategies showed distinct effects: compared with the conventional practice of farmyard manure alone, Haijuneng soil amendment alone was more effective in partially alleviating soil acidification, whereas its combined application with farmyard manure was more favorable for soil organic matter accumulation and enhancing soil phosphorus supply potential.