Areas cultivated with Hass avocado crops in Colombia have growth rapidly. One of the major limitations is the avocado wilt complex disease (AWC) caused by biotic and abiotic factors which have increased under the El Niño southern oscillation ENSO phenomenon (El Niño, La Niña). The objective of this study was to evaluate different strategies for mitigating the adverse effects associated with the ENSO phenomenon and AWC in avocado crops. We evaluated native materials, mulches, and parameters associated with the production of seedlings and planting practices in the field. The response variables tested were plant development, incidence, severity, mortality, and microbial dynamics, among others. The results indicated that native genotypes of Persea americana had different levels of adaptability to drought and flooding conditions. These genotypes also showed some degree of resistance to Phytophthora cinnamomi and Verticillium sp. infection with several degrees of rootstock-scion incompatibility with the Hass cultivar. In addition, mulch reduced the variability of soil moisture and temperature in the soil profile. Adequate selection of genotypes and new tools for planting have decreased the susceptibility to adverse effects associated with the ENSO phenomenon and the incidence and mortality caused by diseases under drought and flooding conditions. This work presents alternatives to mitigate adverse effects of climate variability in avocado crops under tropical conditions.