Abstract Background External Quality Assessment (EQA) programmes, like Quality Control for Molecular Diagnostics (QCMD), allow laboratories to verify the correct functionality of the molecular workflows used in the diagnosis of different pathogens. The aim of this study was to evaluate whether a quick molecular workflow had a good functionality for the diagnosis of different pathogens. Methods A total of 90 frozen samples from 2022 QCMD programmes were analysed. 20 transport medium (TM), 9 TM or saline and 1 saline samples from respiratory panels (QAV164188, QAV164189, QAM174193), 20 synthetic faecal matrix samples from gastrointestinal panels (QAP124154, QAB124153), 13 TM, 4 simulated swabs and 3 urines from sexual transmitted infections (STI) panels (QAB154177, QAM174201), and 18 TM and 2 synthetic cerebrospinal fluid from central nervous system (CNS) panels (QAV174195, QAM174196). Samples were processed using an in-house processing method called quick lysis reagent (QLR) (Certest Biotec S. L.). In parallel, samples were also extracted using the automatic robot KingFisher (Thermo Fisher Scientific). Nucleic acids were analysed at least in duplicate with qPCRs from VIASURE using the CFX96™ Real-Time PCR Detection System (Bio-Rad). Results were compared to the final diagnosis provided by QCMD and with the automatic extractor results. Results The in-house processing method QLR, in combination with VIASURE qPCRs, could process and identify bacteria, parasites and viruses from respiratory, gastrointestinal, STI and CNS panels. Negative samples were correctly detected. This workflow obtained a 100% of sensitive and specificity, same as the automatic extractor. Conclusion These EQA programmes tested the correct functionality of a quick molecular workflow, based on the VIASURE diagnostic products, that could detect different pathogens (bacteria, viruses, and parasites) from different origins (respiratory, gastrointestinal, STI and CNS).