Two partial cleanout methods were compared with complete cleanouts in replicate caged-layer houses for effects on manure characteristics and subsequent dynamics in populations of manure-breeding house fly (Musca domestica L.), lesser mealworm (Alphitobius diaperinus [Panzer]), and associated natural enemies. Absolute densities of adult house flies increased by approximately two to four times within 3 wk after cleanouts of all kinds, and then remained stable over the next 3 mo. Increases were least in barns where residual pads were formed with manure that had been selectively retained from valleys between older piles. Compared with complete cleanouts, partial cleanouts reduced water content of subsequent manure piles. Partial cleanouts also conserved more pteromalid fly parasites, more predatory Xylocoris bugs, and more predatory Carcinops beetles, but not more macrochelid mites. Lesser mealworm populations were reduced by cleanouts of all kinds, but complete cleanouts reduced populations the most. Results suggest choice of cleanout method will depend on whether house flies or lesser mealworms are of primary concern.