Evidence suggests that paternal diet can influence offspring metabolic health intergenerationally but whether dietary animal and plant proteins differ in their impact on fathers and their offspring is not known. Our objective was to examine the effects of a paternal diet high in casein versus pea protein on fathers and their offspring. Five-week-old male rats were fed: 1) control, 2) high animal protein (AP, 36.1% of energy as casein), or 3) high plant protein (PP, 36.1% of energy as pea protein with added methionine) diets for 8-11 weeks before being mated. Offspring were challenged with a high fat/sucrose diet (HFD) from 10-16 weeks of age. Metabolic and microbial outcomes were assessed in both generations. In fathers fed PP diet, enhanced insulin sensitivity and lower liver triglycerides were seen alongside altered hepatic microRNA expression and gut microbial profiles. Few changes were seen in their offspring. In contrast, the paternal AP diet influenced adult offspring hepatic microRNA expression and programmed a latent increase in adiposity, dysregulated satiety hormones, and modified gut microbial composition in their adult offspring that occurred following the HFD. Overall, a diet high in pea protein with added methionine demonstrated protective effects on biomarkers of metabolic health in the fathers but led to minimal effects on the offspring while a paternal diet high in casein led to evidence of an increase in characteristics of metabolic dysfunction in their adult offspring when unmasked by exposure to a HFD for 6 weeks.