The Adenosine triphosphate (ATP) content, dehydrogenase, phosphatase, urease, and beta-glucosidase activity decreased after manure amendment plus solarization (biosolarization), but they recovered after cropping, reaching levels higher than or similar to those before the biosolarization. However, these biochemical parameters decreased and did not recover with time in the methyl bromide (MeBr) treatment. Potential negative soil effects were assayed by measuring, ecotoxicity (Vibrio fisheri luminescence), germination index, electrical conductivity, and heavy metals content. Biosolarization did not negatively affect these parameters, while MeBr application irreversibly decreased the germination index and ecotoxicity. Higher-quality pepper production (extra and first class) were observed with biosolarization but not with MeBr, but no differences were found for pepper yield. Biosolarization gave a Meloidogyne incognita (M. incognita) incidence similar to that of MeBr application.