The coronavirus disease 2019 (COVID-19) has impacted health globally. Cumulative evidence points to long-term effects of COVID-19, such as cardiovascular and cognitive disorders diagnosed in patients even after the recovery period. Micrometer-sized blood clots and hyperactivated platelets have been identified as potential indicators of long COVID. Understanding the composition and prevalence of micrometer-sized clots in the blood is essential for developing diagnostics for the early detection of thrombotic disorders and identifying long-term clinical complications in patients upon SARS-CoV-2 infection. Currently, the detection of microclots in the plasma of COVID-19 pathology relies on fluorescence microscopy-based techniques. In our laboratory, we employ 3D digital holotomography as a label-free technique to study the prevalence and composition of micrometer-sized protein aggregates in the blood of patients with long COVID-19 effects, and the data collected from such an approach can be used to assess disease severity. Our work fulfills an unmet need in the field of blood clot analytics that can be integrated into the clinical pipeline for the early and rapid detection of thrombotic complications in COVID-19, long-term COVID patients, and potentially for screening individuals at risk of cardiovascular diseases.