This study assesses how circadian rhythms of heart rate (HR), HR variability (HRV) and activity change during long-term missions in space and how they relate to sleep quality. Ambulatory 48-h ECG and 96-h actigraphy were performed four times on ten healthy astronauts (44.7 ± 6.9 years; 9 men): 120.4 ± 43.7 days (Before) launch; 21.1 ± 2.5 days (ISS01) and 143.0 ± 27.1 days (ISS02) after launch; and 86.6 ± 40.6 days (After) return to Earth. Sleep quality was determined by sleep-related changes in activity, RR-intervals, HRV HF- and VLF-components and LF-band. The circadian amplitude of HR (HR-A) was larger in space (ISS01: 12.54, P = 0.0099; ISS02: 12.77, P = 0.0364) than on Earth (Before: 10.90; After: 10.55 bpm). Sleep duration in space (ISS01/ISS02) increased in 3 (Group A, from 370.7 to 388.0/413.0 min) and decreased in 7 (Group B, from 454.0 to 408.9/381.6 min) astronauts. Sleep quality improved in Group B from 7.07 to 8.36 (ISS01) and 9.36 (ISS02, P = 0.0001). Sleep-related parasympathetic activity increased from 55.2% to 74.8% (pNN50, P = 0.0010) (ISS02). HR-A correlated with the 24-h (r = 0.8110, P = 0.0044), 12-h (r = 0.6963, P = 0.0253), and 48-h (r = 0.6921, P = 0.0266) amplitudes of the magnetic declination index. These findings suggest associations of mission duration with increased well-being and anti-aging benefitting from magnetic fluctuations.