Recent viral zoonotic epidemics have been attributed partially to the negative impact of human activities on ecosystem biodiversity. These encompass agriculture and specifically conventional agrochemistry-based crop protection (CP) practices. Here we review interactions between CP practices (whether against arthropod or vertebrate pests, plant pathogens, or weeds) and human infectious diseases (whether of bacterial, viral, parasitic, or fungal origin) with a focus on zoonotic diseases, in tropical agroecosystems. Antimicrobial resistance, which is an issue in public health, seems barely affected by conventional CP practices as far as viruses, bacteria, and parasitic protozoa and worms are concerned, but it is a major issue regarding human infections by fungal pathogens. Overall, Agroecological Crop Protection (ACP), by addressing major global challenges including climate resilience, biodiversity conservation, and animal welfare, is the preferred CP strategy for integrating crop plant health within the extended “One Health” concept.