COVID-19 lockdowns resulted in a global shortage of iodinated contrast media. Therefore, alternative imaging protocols were devised to evaluate patients arriving to the emergency department (ED) with suspicion of pulmonary embolism (PE). This quality assurance (QA) aims to compare diagnostic potential between alternative magnetic resonance angiography (MRA) protocol over the gold standard computed tomography angiography (CTA) by evaluating MRA imaging quality, scanner type/imaging sequence, and any risk of misdiagnosis in patients with symptoms of PE. This retrospective study compromised of 55 patients who arrived to ED and underwent MRA of the chest for suspicion of PE during the months of May to June 2022. Data regarding their chief complaints, imaging sequence, and MRA results were collected. Two fellowship-trained faculty radiologists reviewed the MRA scans of the patients and scored the quality using a Likert scale. Two patients were positive for PE and 53 patients showed negative results. Regarding the scan quality issues, motion was noted in 80% of the 55 studies that we reviewed. Significant associations (P < 0.009) between Likert scale scores and initial complaint category were found. The characteristic symptoms associated with suspicion of PE, namely, shortness of breath, chest pain, and cough were distributed among the 1 and 2 categories, reflecting the most optimal vessel opacification scores. We found no risk of misdiagnosis after reviewing the electronic medical record for follow-up appointments within 6 months of ED visit. Patients were screened for PE with MRA as an alternative imaging tool during times of contrast shortage. Further, evaluation of MRA with CTA, side by side, in a larger patient population is required to increase the validity of our QA study.