We verified whether milk thistle seeds and pot marigold seeds provided valuable components for a fibre-rich diet and how their addition affected body composition, nitrogen balance and lipid metabolism in rats. Growing rats were fed a control diet (5% fibre) or three fibre-rich diets (24% fibre), which contained cellulose as the sole source of fibre (24%; positive control), milk thistle seeds (32%) or pot marigold seeds (39%). All diets were balanced in macronutrients, including total protein content (9%), which was half of the amount recommended for rats to maximise protein absorption and utilisation, and the ratio of plant protein to animal protein (approx. 1:1). After 4 weeks, dietary pot marigold seeds reduced body weight gain, which translated into lower gains of body fat and lean mass in rats (all at p ≤ 0.05). Protein digestibility differed among individual fibre-rich diets (p ≤ 0.05), with the lowest result having been recorded for dietary pot marigold seeds (73%), followed by dietary milk thistle seeds (78%), and the highest result having been recorded for dietary soybean protein isolate (control protein source, 89%). Nitrogen retention was higher with dietary soybean protein isolate (53%) and dietary milk thistle seeds (47%) than with dietary pot marigold seeds (38%) (p ≤ 0.05). In the caecal digesta, the concentrations of the major short-chain fatty acids were almost or >2-fold higher after dietary milk thistle seeds and pot marigold seeds than after the positive control diet (all at p ≤ 0.05). Dietary pot marigold seeds enlarged the liver and increased the plasma activities of liver enzymes but reduced hepatic lipid contents (all at p ≤ 0.05). Certain Asteraceae seeds provide components of varied nutritional quality, with milk thistle seeds being a relatively good source of protein and both types of seeds being a source of fermentable fibre. Pot marigold seeds have potential anti-obesogenic effects, but with the risk of damaging internal organs.