In late 2019, a new virus, SARS-CoV-2, emerged in Wuhan, China, causing COVID-19 and the subsequent global pandemic. As of 30 April 2023, more than 774 million cases of COVID-19 had been reported worldwide, including over 7.5 million in Mexico. Despite advances in vaccination, epidemic surges of COVID-19 continued to occur globally, highlighting the importance of sharing and disseminating the experiences gained during these first years to better understand the virus’s evolution and respond accordingly. For this reason, the National Council for Science and Technology (CONACYT) organized the meeting “Challenges and Opportunities for Genomic Surveillance of SARS-CoV-2 in Mexico” from 15 to 17 August 2022, to present the efforts and results accumulated over more than two years of the pandemic. In this meeting report, we summarize the key findings of each participant and provide their contact information.