This study aimed to measure hemolysis before, during and after 60 days of the ground-based spaceflight analog bed rest and the effect of a nutritional intervention through a prospective randomized clinical trial. Twenty male participants were hospitalized for 88 days comprised of 14 days of ambulatory baseline, 60 days of 6° head-down tilt bed rest and 14 days of reambulation. Ten participants each received a control diet or daily polyphenol associated with omega-3, vitamin E, and selenium supplements. The primary outcome was endogenous carbon monoxide (CO) elimination measured by gas chromatography. Hemolysis was also measured with serial bilirubin, iron, transferrin saturation blood levels and serial 3-day stool collections were used to measure urobilinoid excretion using photometry. Total hemoglobin mass (tHb) was measured using CO-rebreathing. CO elimination increased after 5, 11, 30, and 57 days of bed rest: +289 ppb (95% CI 101–477 ppb; p = 0.004), +253 ppb (78–427 ppb; p = 0.007), +193 ppb (89–298 ppb; p = 0.001) and +858 ppb (670–1046 ppb; p < 0.000), respectively, compared to baseline. Bilirubin increased after 20 and 49 days of bed rest +0.8 mg/l (p = 0.013) and +1.1 mg/l (p = 0.012), respectively; and iron increased after 20 days of bed rest +10.5 µg/dl (p = 0.032). The nutritional intervention did not change CO elimination. THb was lower after 60 days of bed rest −0.9 g/kg (p = 0.001). Bed rest enhanced hemolysis as measured through all three by-products of heme oxygenase. Ongoing enhanced hemolysis over 60 days contributed to a 10% decrease in tHb mass. Modulation of red blood cell control towards increased hemolysis may be an important mechanism causing anemia in astronauts.