The objective of this work was to evaluate microwave heating (MW) in the processing of camu‐camu juices. A factorial design (2²) with repetition at the central point was performed. We evaluated the effect of microwave power (310‐940 W) and processing time (15‐45 s) on physicochemical characteristics, reduction of enzyme activity (POD and PPO), microbiological quality and bioactive compounds content (DPPH, phenolic compound, ascorbic acid, and anthocyanins). Generally, the juices treated by MW presented better results in comparison to the conventional method. There were no significant changes in pH, titratable acidity, total soluble solids, and color parameter in camu‐camu juices in comparison with untreated samples. The ascorbic acid content in the juices increased after the treatment by MW. A significant reduction of degrading microorganisms was observed for the treated juice in relation to the control juice. Microwave heating can be a good alternative for the treatment of Amazonian fruit juices. PRACTICAL APPLICATIONS: The global consumer market requires that foods be high in bioactive compounds to improve human health. The Amazon Rainforest is known worldwide for its rich biodiversity, mainly for its wide variety of foods rich in bioactive compounds. The lack of transportation infrastructure and basic sanitation in the region causes the food to present high microbial contamination that can accelerate food degradation, especially its bioactive compounds. The use of microwave heating may be an opportunity to offer a fast, efficient, and low‐cost process for the reduction of microorganisms in fruit juices and pulps. This study is a pioneer in the use of emerging technologies in the conservation of Amazonian fruit juices, allowing a new opportunity for the food industry to offer products with high nutritional value.