Agriculture plays a critical role in Uganda’s economy, contributing to 24% of the gross domestic product (GDP) and serving as the primary source of livelihood for a large portion of the population. Organic horticulture presents a promising pathway for sustainable development, offering economic opportunities through access to niche markets both locally and internationally. However, effective management for pests and diseases remains a major challenge in organic horticulture. This review addresses pest and disease issues affecting non-traditional export crops in Uganda, such as pepper, bitter gourd, and aubergine. Additionally, it provides an overview of botanical pesticides currently used in Uganda, along with approved organic fungicides (e.g., lime sulfur, copper) and insecticides (e.g., paraffinic oils, pyrethrum). This review explores physical and chemical properties, target pests, benefits, drawbacks, and active ingredients of these substances. The ultimate aim is to offer Ugandan farmers expanded options for managing pests and diseases in organic horticulture.