In a bid to develop technologies that serve grower needs for economic management of pests and diseases of hot pepper (scotch bonnet) while protecting public health and the environment, a study to assess the potential of cover cropping and/or less-risk pesticide usage in the management of pests and diseases of hot pepper was conducted for two consecutive seasons in Uganda. A split-plot randomized complete block design with three replications was used with cropping system (main plots) and pesticide treatment (sub-plots) as the factors. There were two cropping systems: the hot pepper+cowpea system vs. a hot pepper monocrop and five pesticide treatment options: (i) prophylactic treatment of plots at transplanting with granular carbofuran; (ii) weekly sprays of a neem-based formulation; (iii) combination of the prophylactic carbofuran treatment and neem; (iv) sulphur sprays at 10-day intervals (season 2 only); and (v) the untreated control. Data were collected on population dynamics of aphids, whiteflies, thrips, mites, nematodes and on plant performance parameters of branching and fruit weight. Results indicated that the hot pepper+cowpea system greatly lowered infestations of aphids and nematodes on hot pepper, but did not decrease thrips and whiteflies; and brought about a yield penalty on hot pepper. Prophylactic applications of carbofuran and/or sprays of a neem-based formulation lowered populations of aphids and whiteflies on hot pepper to varying extents; and increased yield of pepper.