Neck circumference (NC), neck circumference to height ratio (NHtR) and neck circumference to weight ratio (NWtR) appear to be good candidates for the non-invasive management of non-alcoholic fatty liver disease (NAFLD). This study aimed to evaluate the ability of routine variables to assess and manage NAFLD in participants with obesity and NAFLD included in a 2-year nutritional intervention program. Anthropometric measurements, biochemical variables and imaging techniques were performed at different study time-points (baseline, 6, 12 and 24 months). The nutritional intervention significantly improved all anthropometric measurements as well as the glucose profile and the hepatic enzymes. NC and neck ratios combined with ALT levels and HOMA-IR showed good prediction ability for the hepatic fat content and hepatic steatosis at all the study time-points in a ROC analysis. The prediction ability of the combination panels improved when the weight loss variable was also considered. NC and neck ratios are easy anthropometric measurements that in combination with routine biochemical variables (ALT and HOMA-IR) showed good prediction ability of NAFLD. More research studies are necessary to validate the utility of these simple and easy variables as surrogate markers of NAFLD since their application could improve the prevention and management of this prevalent disease.