Background <p>Lebanon experienced a severe economic crisis, exacerbated by the COVID-19 pandemic and the Beirut port explosion in August 2020. This crisis pushed over half of the population into poverty resulting in widespread food insecurity. The latter often leads to inadequate intake of essential micronutrients such as vitamin B12 and folate. The aim of this study is to investigate and compare the influence of the economic crisis on the prevalence of these micronutrient deficiencies.</p> Methods <p>This retrospective study, conducted at Al Zahraa Hospital University Medical Center in Beirut, investigated the impact of Lebanon’s economic crisis on the prevalence of vitamin B12 and folate deficiencies. Data from 3,116 participants who underwent vitamin B12 and/or folate testing between January 2018 and June 2022 were analyzed. The study aimed to compare the prevalence of these deficiencies before (2018–2019) and during the crisis (2020–2022).</p> Results <p>Results showed no significant change in folate levels or deficiency prevalence during the crisis. However, there was a notable increase in vitamin B12 deficiency, from 9.8% before the crisis to 14% during the crisis. Male patients and young adults were more likely to experience folate and vitamin B12 deficiencies, respectively. The findings highlight the crisis's detrimental impact on food security and nutritional health in Lebanon, particularly concerning vitamin B12 deficiency.</p> Conclusions <p>In conclusion, this study underscores the importance of addressing food security to prevent micronutrient deficiencies and their associated health risks in crisis-affected populations. The significant rise in vitamin B12 deficiency during the economic crisis in Lebanon calls for urgent public health interventions.</p>