Food pantries are an important source of food for those facing food insecurity. The Charitable Food Nutrition Index (CFNI) was developed for research and practice to measure the nutritional quality of assortments of foods in this setting. The study assessed the construct validity of the CFNI using secondary data from a group-randomized food pantry intervention in Minnesota. The CFNI was calculated for each client cart post-intervention (n = 187; 85 intervention, 102 control). CFNI scores were based on the proportion of items in each client cart ranked “green,” “yellow,” or “red” using the Healthy Eating Research Nutrition Guidelines for the Charitable Food System. An implementation score assessing intervention fidelity was measured for each pantry (n = 11; 5 intervention, 6 control) based on the four intervention subcomponents: aesthetics/use of space; healthy food prominence and appeal; unhealthy food de-emphasis; and stocking standards. Mixed linear models were used to test whether: (a) client carts from pantries in the intervention condition had higher CFNI scores than those in the control condition, and (b) higher implementation scores were associated with higher CFNI scores. In adjusted models, clients from intervention group pantries had higher CFNI scores, reflecting a healthier assortment of foods compared with clients from control group pantries (p = 0.022). CFNI scores were positively associated with greater fidelity to the intervention (p = 0.020). The CFNI was sensitive enough to detect the effects of the intervention in the expected directions. These findings support its construct validity and utility as a measure in the charitable food system.