The effects of two waste sources, red hybrid tilapia (Oreochromis sp.) and whiteleg shrimp (Litopenaeusvannamei), and two drying methods (freeze-drying and oven-drying) on the proximate chemical composition of bioflocs were investigated. In total, four kinds of experimentally treated bioflocs were compared to identify the best waste source and drying method to produce biofloc of an acceptable nutrient value: freeze-dried shrimp biofloc (FDSBF), oven-dried shrimp biofloc (ODSBF), freeze-dried tilapia biofloc (FDTBF), and oven-dried tilapia biofloc (ODTBF). The protein, lipid, ash, fiber, total nitrogen free extract (NFE), and energy contents of the dried bioflocs ranged from 12.12 to 24.09 g/100 g, 0.35 to 0.92 g/100 g, 42.45 to 61.01 g/100 g, 7.43 to 17.11 g/100 g, 16.45 to 18.59 g/100 g, and 0.99 to 1.94 Kcal g−1, respectively. Statistically, there were significant differences within the means of the two biofloc sources in terms of their proximate compositions (p < 0.05). The average values between the drying methods for protein, lipid, total NFE, and energy were also significantly different, while no significant differences (p > 0.05) were recorded for ash and fiber. Amino acids (AAs) were higher in FDTBF, followed by ODTBF. The mineral profiles showed that phosphorous, potassium, manganese, selenium, and copper were higher in the tilapia waste bioflocs, while calcium, zinc, iron, copper, chromium, and cobalt were higher in the shrimp waste bioflocs. Although the statistical analysis showed that the shrimp waste bioflocs had higher levels of lipid, fiber, total NFE, and minerals, the tilapia waste bioflocs contained higher levels of potential AAs, energy, and protein, which are regarded as expensive ingredients in aquaculture feeding. This study indicates that biofloc derived from tilapia waste can be regarded as a more suitable source of biofloc meal (in terms of protein, ash, energy, and AAs) than biofloc derived from shrimp waste. Our findings also suggest that freeze-drying is a more effective drying method for drying biofloc, as it efficiently maintains nutritional quality.