Abstract External quality assessment (EQA) is an essential part of performance monitoring for molecular laboratories. At the moment, a national law regulates participation in EQA schemes for clinical biology and pathology in Belgium. This study aimed (1) to get insights on how laboratories organize their EQA participation, (2) to poll satisfaction with the current situation (selection of EQA programs in advance by a governmental body), (3) to provide guidance for choosing the most relevant EQA provider and (4) to propose a new model for national performance monitoring. A survey was sent to Belgian laboratories performing molecular tests in the field of microbiology, hematology and pathology with (1) general questions on how they select an EQA provider and (2) their satisfaction of each provider. In total, 25 molecular laboratories [microbiology ( N = 13), hematology ( N = 8) and pathology ( N = 4)] from 14 different hospitals completed the survey regarding their EQA organization. All three laboratory groups indicated to prefer EQA schemes using real patient materials as well as those with varying targets and concentrations. For molecular microbiology and hematology, schemes with a syndromic approach are sought. Since annual participation in EQA becomes burdensome in most laboratories, this paper also offers a risk-based strategy for determining the participation frequency. Based on the needs of Belgian laboratories, three proposals were made: (1) for the proper selection of an EQA scheme, (2) for determining the minimal participation frequency and (3) for the national organization of EQA schemes.