The objective of this study was to assess whether the Brazilian Workers' Food Program (WFP) is associated with changes in the nutritional status of workers in the transformation industry. We conducted a cross-sectional, observational, comparative study, based on prospectively collected data from a combined stratified and two-stage probability sample of workers from 26 small and medium size companies, 13 adherent and 13 non-adherent to the WFP, in the food, mining and textile sectors. Study variables were body mass index (BMI), waist circumference (WC), and dietary intake at lunch obtained by 24-hour dietary recall. Data were analyzed with nested mixed effects linear regression with adjustment by subject variables. Sampling weights were applied in computing population parameters. The final sample consisted of 1069 workers, 541 from WFP-adherent and 528 from WFP non-adherent companies. The groups were different only in education level, income and in-house training. Workers in WFP-adherent companies have greater BMI (27.0 kg/m2 vs. 26.0 kg/m2, p = 0.002) and WC (87.9 cm vs. 86.5, p = 0.04), higher prevalence of excessive weight (62.6% vs. 55.5%, p<0.001) and of increased WC (49.1% vs. 39.9%). Workers of WFP companies have lower intake of saturated fat (-1.34 g, p<0.01) and sodium (-0.3 g, p<0.01) at lunch. In conclusion, this study showed that workers of companies adherent to the Brazilian WFP have greater rates of excessive weight and increased cardiovascular risk-a negative finding-as well as lower intake of sodium and saturated fat-a positive finding. Therefore, the WFP needs to be revisited and its aims redefined according to the current epidemiological status of the target population of the program.