Worldwide, honey bees are increasingly faced with periods of pollen scarcity, which can lead to nutritional deficiencies, especially of proteins and amino acids. These are essential for the proper functioning of the single organism and the colony. To understand how bees react to protein deficiency, under controlled conditions, we studied the effect of pollen deficiency on the main physiological parameters in two subspecies endemic of Algeria, Apis mellifera intermissa and Apismellifera sahariensis. Emerging workers of both subspecies were reared with two diets: one was pollen-fed, whereas the other pollen-deprived. Several physiological criteria were measured depending on the type of diet and subspecies: the survival of the bees, the amount of total protein in the hemolymph, hypopharyngeal glands development and the ovary development of workers. These last three parameters were assessed at three different ages (7, 14 and 21 days). At birth, sahariensis workers weighed more than intermissa. With the same protein diet, the average life expectancy of sahariensis was extended by 5.55 days compared to intermissa. Even if deprived of pollen, sahariensis lived longer than intermissa fed with pollen (p < 0.001). In the three age levels, the hypopharyngeal glands were more developed and less affected by pollen deficiency (p < 0.001) in sahariensis than in intermissa (p < 0.001). The total hemolymph protein was higher in intermissa than in sahariensis regardless of the diet, and was also higher in protein-fed than in deprived bees (p < 0.001). The ovaries developed more rapidly with a high proportion in intermissa than in sahariensis (p < 0.05) regardless of the diet, and was also higher in the bees fed with pollen than those deprived (p < 0.05). Pollen deficiency generates physiological alterations and modifications, the amplitude of which varied according to the subspecies of the bee studied.