Introduction: We aimed at validating a harmonized protocol for monitoring occupational exposure to engineered/incidental nanoparticles (EINP) and to assess their health effects. Materials and Methods: A multicentric prospective cohort study was designed involving repeated field campaigns of 4-day exposure monitoring and two biological samplings, at the beginning (T1) and at the end (T2) of working week. To detect a significant difference in effect biomarkers of at least 25%, a sample size of 120 workers (60 exposed, 60 non-exposed) was determined, along with two control groups, internal and external to company. The protocol feasibility was tested in three countries: Switzerland, Spain, and Italy. Number and mass concentration, morphology, size distribution and surface area of EINP were measured, and effect biomarkers (oxidative stress and inflammation) were assessed in exhaled breath condensate (EBC) and/or urine samples. Results: The preliminary results of 42 external controls showed no significant change in effect biomarker levels between T1 and T2, with the exception of malondialdehyde and 8-Isoprostane in EBC. The biomarkers levels were within the ranges reported in healthy adults. The analysis of data and samples collected in 60 exposed workers and 36 internal controls recruited at six EINP-handling facilities are ongoing. Conclusions: These findings confirm the feasibility of the harmonized protocol. For its implementation, a particular effort on organization, coordination and communication between each team was mandatory, particularly during COVID time.