In this field study, the fungicidal and nematicidal activity of two plant extracts (Larrea spp. (LR), Liquidambar spp. (LQ)), and an organosulfur soil fungicide metam sodium alone (MS), and a mix of LR and MS (LR + MS) was assayed under pepper cropping in southeastern Spain. Metam sodium treatments (MS and LR + MS) produced the highest crop yields and were more effective in controlling root-knot nematodes and fungal pathogens (Fusarium, Pythium, and Rhizoctonia solani) than the plant extracts treatments (LQ and LR). Furthermore, the effect of the metam sodium treatments applied negatively affected the soil microbial community, principally bacteria, but not fungi. These microbial community changes of the soil were principally observed after treatment application; the differences between the treatments were reduced at the end of the experiment, when recovery of the soil microbiota communities occurred.