Peripheral arterial disease (PAD) is a highly prevalent disease process that afflicts more than 20% of individuals with diabetes. Progression of PAD in the setting of diabetes can lead to critical limb ischemia (CLI), which is associated with increased risk of wounds, gangrene, and limb loss. Prompt noninvasive evaluation of limbs affected by PAD progression and CLI is currently limited. Here, we evaluate the utility of a custom-designed multispectral imaging system for fluorescence-based near-infrared angiography and compare it to the existing gold standard of laser-scanning Doppler perfusion assessments. Due to its higher resolution and fluorescence sensitivity, near-infrared angiography demonstrates a greater capacity to characterize altered dynamic arterial perfusion in a clinically relevant diabetic murine model for CLI. Furthermore, we demonstrate that our imaging system can accurately track arterial perfusion recovery over time following induced ischemia, and reveal unique phenotypic differences in the setting of diabetes.