The effects of deep-frying and oven-baking on chemical, physical, and microbiological, properties of cassava croaker (Pseudotolithus senegalensis) nuggets during frozen storage were investigated. The moisture, protein, fat, ash, and carbohydrate contents varied among the cooking methods and frozen storage times. The deep-fried nugget had a higher fat content, which resulted in a higher energy value (p < 0.05). The free fatty acid content and peroxide value (PV) of the oven-baked nuggets were higher than the deep-fried ones (p < 0.05). The PV tended to increase with increasing storage time, but it was still within the recommended range for consumption. The deep-fried nugget showed a vivid orange–yellow color, with higher L*, a*, and b* values, while oven-baked nuggets showed a pale-yellow color. The baked nuggets had relatively lower total expressible fluid than the deep-fried nuggets at all time points (p < 0.05). The hardness, springiness, and chewiness of deep-fried nuggets were higher than baked nuggets throughout the storage period (p < 0.05). The total plate count and yeast and mold counts produced by the two cooking methods were within the acceptable range throughout the storage.