Background: Fathers’ mental and physical health is important for men’s well-being, as well as for their partner’s and children’s health. The study objectives were to describe how expectant fathers experienced physical and emotional changes, the prevalence of the changes, and whether the sensations changed over time. Methods: We used a longitudinal study with a mixed-method approach that included quantitative and qualitative data collected by questionnaires completed in their partner’s mid-pregnancy and late pregnancy. Descriptive and inferential statistics and content analysis were used. Results: In total, 871 Swedish expectant fathers participated. The proportion of emotional changes decreased from 60% in mid-pregnancy to 47% in late pregnancy (P < 0.001), and these changes included positive and negative impact on mental health, the emotional relationship developed with the partner and unborn baby, and reflections of fatherhood. Physical changes experienced increased from 12% in mid-pregnancy to 18% in late pregnancy (P = 0.001) and involved negative and positive aspects, or no impact on physical health. Physical changes reported implied change in the sexual relationship. Conclusions: More than half the expectant fathers experienced some degree of emotional change during their partner’s pregnancy, and one in five experienced physical changes. Emotional and physical changes affected the expectant fathers’ mental and physical health. Expectant fathers seem to undergo a vulnerable process leading to fatherhood.