Semen analysis is characterized by high levels of intra- and inter-laboratory variability, due to a low level of standardization, high subjectivity of the assessments, and problems with automated procedures. To improve consistency of laboratory results, quality control and training of technicians are important requisites. The goals of this study are to evaluate the results of an external quality control (EQC) program and standardized training by ESHRE Basic Semen Analysis Courses (BSAC) on the variability in manual assessments of semen parameters. We performed retrospective analyses of (1) the interlaboratory variability in the Dutch EQC program and (2) the interobserver variability in BSACs for concentration, motility, and morphology assessments. EQC data showed that the interlaboratory coefficient of variation (CV) for concentration assessment decreased (range from 24.0%–97.5% to 12.7%–20.9%) but not for morphology and motility assessments. Concentration variability was lower if improved Neubauer hemocytometers were used. Morphology assessment showed highest CVs (up to 375.0%), with many outliers in the period of 2007–2014. During BSAC, a significant reduction of interobserver variability could be established for all parameters (P < 0.05). The absence of an effect in the EQC program for motility and morphology might be explained by respectively the facts that motility assessment was introduced relatively late in the EQC program (since 2013) and that criteria for morphology assessment changed in time. BSAC results might have been influenced by the pretraining level of participants and the influence of external factors. Both EQC and training show positive effects on reducing variability. Increased willingness by laboratories to change their methods toward standards may lead to further improvements.