Abstract Objectives Even though 90% of the prison population is male, fatherhood among prisoners is an overlooked topic. Previous studies suggest that experienced severity of detention is different between fathers and non-fathers in prison because there is a unique deprivation strain related to fatherhood. There are criminological arguments and arguments in the legal context why we need more knowledge on the experience of detention by incarcerated fathers. Methods We studied longitudinal data of 785 males in pre-trial detention in the Netherlands from the nationwide Prison Project study population: 329 fathers were compared with 456 non-fathers for experienced severity, adjustment patterns (i.e. mental distress and misconduct), and deprivations strains. Results We found differences between fathers and non-fathers, both in adjustment and deprivation strains. Fathers reported less adjustment problems and different deprivation strains than non-fathers. Missing children during pre-trial detention was associated with depressive behavior (β = 0.158, p < 0.005) and anxiety among fathers (β = 0.128, p < 0.05). Conclusions Our results underline the importance of designing interventions for fathers in prison and educating sentencers about this topic. Proportional sentencing of fathers in the criminal justice system could only be validated as long as sufficient attention will be paid to their unique deprivation strain, which is, missing their children. During pre-trial detention, care for the child-father relation may not only lead to father’s emotional wellbeing during pre-trial detention, but may also lead to strengthened family bonds and children’s wellbeing on the long term.