As technological advancements in extended reality (XR) amplify the demand for more XR content, traditional development processes face several challenges: 1) a steep learning curve for inexperienced developers, 2) a disconnect between 2D development environments and 3D user experiences inside headsets, and 3) slow iteration cycles due to context switching between development and testing environments. To address these challenges, we introduce AtomXR, a streamlined, immersive, no-code XR prototyping tool designed to empower both experienced and inexperienced developers in creating applications using natural language, eye-gaze, and touch interactions. AtomXR consists of: 1) AtomScript, a high-level human-interpretable scripting language for rapid prototyping, 2) a natural language interface that integrates LLMs and multimodal inputs for AtomScript generation, and 3) an immersive in-headset authoring environment. Empirical evaluation through two user studies offers insights into natural language-based and immersive prototyping, and shows AtomXR provides significant improvements in speed and user experience compared to traditional systems.