Preliminary studies suggest that a modified Paleolithic diet may benefit symptoms of fatigue in progressive multiple sclerosis (MS). However, this diet restricts the consumption of eggs, dairy, and gluten-containing grains, which may increase the risk of micronutrient deficiencies. Therefore, we evaluated the nutritional safety of this diet among people with progressive MS. Three nonconsecutive 24-h dietary recalls were collected from (n = 19) progressive MS participants in the final months of a diet intervention study and analyzed using Nutrition Data System for Research (NDSR) software. Food group intake was calculated, and intake of micronutrients was evaluated and compared to individual recommendations using Nutrient Adequacy Ratios (NARs). Blood was drawn at baseline and the end of the study to evaluate biomarker changes. Mean intake of fruits and vegetables exceeded nine servings/day and most participants excluded food groups. The intake of all micronutrients from food were above 100% NAR except for vitamin D (29.6 ± 34.6%), choline (73.2 ± 27.2%), and calcium (60.3 ± 22.8%), and one participant (1/19) exceeded the Tolerable Upper Limit (UL) for zinc, one (1/19) for vitamin A, and 37% (7/19) exceeded the chronic disease risk reduction (CDRR) for sodium. When intake from supplements was included in the analysis, several individuals exceeded ULs for magnesium (5/19), zinc (2/19), sodium (7/19), and vitamins A (2/19), D (9/19), C (1/19), B6 (3/19), and niacin (10/19). Serum values of vitamins D, B12, K1, K2, and folate significantly increased compared to respective baseline values, while homocysteine and magnesium values were significantly lower at 12 months. Calcium and vitamin A serum levels did not change. This modified Paleolithic diet is associated with minimal nutritional risks. However, excessive intake from supplements may be of concern.