Due to the intensification of the poultry sector, poultry manure is being produced in increasing quantities, and its on-site management is becoming a critical problem. Animal health problems can be solved by stricter the veterinary and environmental standards. The off-site coupled industrial chicken manure recycling technology (Hosoya compost tea) fundamentally affects the agricultural value of new organic-based products. Due to the limited information available on manure recycling technology-related microbiological changes, this was examined in this study. A pot experiment with a pepper test plant was set up, using two different soils (Arenosol, slightly humous Arenosol) and two different doses (irrigation once a week with 40 mL of compost tea: dose 1, D1; irrigation twice a week with 40 mL of compost tea: dose 2, D2) of compost tea. Compost tea raw materials, compost tea, and compost tea treated soils were tested. The products (granulated manure, compost tea) and their effects were characterized by the following parameters: aerobic bacterial count (log CFU/g), fluorescein diacetate activity (3′,6′-diacetylfluorescein, FDA, µg Fl/g soil), glucosidase enzyme activity (GlA; PNP/µmol/g), and identification of microorganisms in compost tea with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, we aimed to investigate how the microbiological indicators tested, and the effect of compost tea on the tested plant, could be interpreted. Based on our results, the microbiological characteristics of the treated soils showed an increase in enzyme activity, in the case of FDA an increase +0.26 μg Fl/g soil at D1, while the GlA increased +1.28 PNP/µmol/g with slightly humous Arenosol soil and increased +2.44 PNP/µmol/g at D1; and the aerobic bacterial count increased +0.15 log CFU/g at D2, +0.35 log CFU/g with slightly humous Arenosol and +0.85 log CFU/g at W8. MALDI-TOF MS results showed that the dominant bacterial genera analyzed were Bacillus sp., Lysinibacillus sp., and Pseudomonas sp. Overall, the microbial inducers we investigated could be a good alternative for evaluating the effects of compost solutions in soil–plant systems. In both soil types, the total chlorophyll content of compost tea-treated pepper (Capsicum annuum L.) had increased as a result of compost tea. D1 is recommended for Arenosol and, D2 for slightly humous Arenosol soil.