Enhanced growth and survival indicate a quality diet important in the production of quality fish larvae. Diet’s quality heavily depends on the quality of its protein which varies with inclusion levels and sources. This Influences stress responses and compromises wellbeing larvae due to diets suboptimal provision of nutritional requirements. However, there exists a knowledge gap on the performance of different proteins beyond growth and survival. The objective of this study was to determine the effects of partially replacing Caridina nilotica with Spirulina platensis or Eisenia fetida on stress tolerance of Clarias gariepinus larvae. This was conducted in 0.0, 0.3, 0.5, 0.7mg/l ammonia concentrations at 28°C and pH 7 within 24-hours using four- and six-weeks old larvae. The larvae were fed on formulated diets and a control at 10% body weight, five times a day. All larvae exposed to 0.7mg/l ammonia concentration died irrespective of the diet fed. A combination of 50%Caridina nilotica and 50%Eisenia fetida fed larvae posted low (p<0.001) total mortality of 78% and 52% in 0.5mg/l, stress indices of 457.3 and 342 and, took the longest time of 12.67 and 18.67-hours for half the number of larvae exposed to die in 0.7mg/l ammonia respectively for four- and six-week-old larvae. However, larvae fed on 50%Spirulina platensis and 50%Caridina nilotica posted higher (p<0.001) total mortality of 97% and 73% in 0.5mg/l, stress indices of 574.3 and 476.3 and, shortest time of 8 and 10.17-hours for half the number of 4- and 6-weeks old (respectively) larvae exposed to 0.7mg/l ammonia to die. Protein source influenced stress tolerance with Eisenia fetida diets enhancing better larvae tolerance to ammonia compared to Spirulina platensis and Caridina nilotica (control) diets. Caridina nilotica could be replaced by Eisenia fetida up to 50% and 25% by Spirulina platensis to enhance Clarias gariepinus larvae tolerance to ammonia stress.