The use of fruits and their by-products in food has dramatically impacted the food industry due to the nutritional benefits and the technological and sensory effects of food matrices. Therefore, this research aimed to evaluate the effects of adding cupuassu (Theobroma grandiflorum) pulp and flour on fermented milk beverages’ physicochemical, microbial, and sensory properties during refrigerated storage (0, 7, 14, 21, and 28 days). Twelve formulations were realized with different percentages of cupuassu pulp (0, 5, 7.5, and 10%w/v) and flour (0, 1.5, and 3%w/v). The treatments with 3% cupuassu flour presented the highest percentages of protein, fat, fiber, and carbohydrates, compared with the samples containing pulp. On the other hand, the addition of pulp increased water retention capacity and color parameters (L*,a*,b*, andC*) and decreased pH and syneresis on day 0 of storage. During storage, the samples with pulp showed increases in pH values, consistency index, and apparent viscosity. In comparison, cupuassu flour addition decreased syneresis values and increasedL*andb*during storage, as did pulp. In addition, sample HPHF (10% pulp and 3% cupuassu flour), based on just-about-right, penalty, and check-all-that-apply analyses, improved some sensory attributes of the fermented milk beverage, such as brown color, acid taste, bitter taste, cupuassu flavor, and firm texture. It can be concluded that cupuassu pulp and flour addition improves the physicochemical and sensory quality of fermented milk beverages and can provide nutritional value to the product.