<p><i>Chaoborus edulis</i> (Lake flies) are abundant along Lake Malawi and offer a promising solution to food and nutrition insecurity. However, the effects of traditional processing methods on their nutritional quality and acceptability remain largely unknown. This study assessed the nutritional composition and consumer acceptability of <i>C. edulis</i> processed by baking, boiling, and pan-frying. A cross-sectional, mixed-methods study was conducted, combining laboratory-based analyses of nutritional content using standard AOAC methods with qualitative assessments of sensory acceptability using a standardized 9-point hedonic scale. Nutritional content data were analyzed using One-way Analysis of Variance (ANOVA), while sensory rating data were analyzed using the Kruskal–Wallis test. Crude protein content varied significantly across the three processing methods (<i>p</i> &lt; 0.05), with baked <i>C. edulis</i> exhibiting the highest protein levels (55.13 ± 0.14%) and pan-fried the lowest (44.67 ± 0.44%). Calcium content exhibited significant differences across processing methods (<i>p</i> &lt; 0.05). Overall, baking method yielded the highest nutrient retention. Despite this, pan-fried <i>C. edulis</i> was the most preferred for its taste, texture, appearance, and aroma. These findings indicate a trade-off between nutritional value and consumer preference, with baking being superior for nutrient preservation, while pan-frying enhances sensory acceptability. The study highlights the potential of baked <i>C. edulis</i> as a nutrient-dense food option suitable for integration into food systems. Its appreciable crude protein content may help address protein deficiencies prevalent among children and women in low-income settings, while its calcium content contributes to improved bone health. Baking is recommended as the preferred processing method due to its superior nutrient retention.</p>