Synthetic insecticides heavily applied to manage agricultural pests are highly hazardous to the environment and non-target organisms. Their overuse through repeated treatments in smallholder farming communities is frequent. Botanical biopesticides are ideal for sustainable pest management in agricultural environments by keeping synthetic insecticide use at a minimum. Here we evaluated a locally prepared neem seed extract (NSE) alongside emamectin benzoate against both lepidopteran pests Helicoverpa armigera (Hübner) and Spodoptera exigua (Hübner) on tomato Lycopersicon esculentum Mill under natural field conditions in Pakistan. We compared pest severity, fruit injury, quality, marketability, and cost:benefit ratio (CBR) between treatments. The concentration of azadirachtin A in the NSE was 26.5 ppm. NSE at 2% (20 mL/L) and the emamectin benzoate at the recommended field rate in Pakistan were sprayed weekly throughout the fruiting stage. The pest larvae were significantly more abundant on fruits than on flowers and leaves. Fruit injury and losses were significantly more important in untreated control compared to NSE and emamectin benzoate treatments. NSE efficacy varied with respect to the cultivars used and the seasons. Cultivar Eden harboured more pests than Adventa, and emamectin benzoate suppressed more pest individuals than NSE. Both the insecticidal treatments were comparable in terms of marketable yield productions as well as unmarketable, uninjured, and recovered fruit yields. NSE generated a higher CBR (1: 9.26) than emamectin benzoate (1: 3.23). NSE suppressed pests by acting as an antifeedant, similar to its synthetic counterpart. Smallholder growers can thus use NSE as a cost-effective solution in tomato pest management in Pakistan.