Embedded devices play a major role in supporting critical infrastructure, but lack many of the security pro-tections of sophisticated systems. Determining whether these devices are compromised is, therefore, a challenge. In this work, we describe a novel control flow verification methodology via electromagnetic (EM) emanations. We design a framework that incorporates signal processing and training to detect subtle control flow deviations as small as three clock cycles, the minimum required to execute a return with malicious activity on modern embedded hardware. Our methodology leverages basic block detection, enabling the discovery of these subtle control flow deviations that escape conventional detection approaches. We evaluate our framework's ability to detect insertion and modification control flow attacks on six different case studies of real-world critical operations and two processors featuring different architectures. Our results show 96.6% detection accuracy across all tested programs and attacks. Finally, we show the transferability of our methodology to different instances of our evaluated processors, reaching up to 98.7% convergence with our baseline models while requiring a third of the collected EM samples compared to standard retraining. In doing so, we reveal the feasibility of fine-grained EM-based control flow monitoring for low-power microcontrollers.