Military families are faced with specific challenges associated with the professional military context, such as the separation of the military member from the rest of the family, because of participation in international missions. This exploratory, qualitative study investigates the association between participation in such missions—before, during and after deployment—and marital relationships and parenting in Portuguese military families. A thematic analysis of interviews with 13 military’s spouses indicates that in the pre-deployment phase children are prepared for the physical absence of the military parent, as emphasis is placed on clear communication that promotes the parent-child relationship. Some days before separation, the couple become closer and more intimate, enjoying their last moments alone. During deployment, the main challenges are the additional parental tasks and responsibilities of the parent who stays at home, insecurity regarding the marital relationship and a common concern for the deployed partner’s well-being. On the other hand, the absence of the military parent may provide an opportunity for both the parent-child and couple relationships to be strengthened. During this phase the main resources used are communication technologies, which enable the absent parent/partner to be present psychologically and emotionally, as well as social support and personal resources/strengths. In the post-deployment phase, reintegration of the military member presents itself as a challenge to the family structure, and reorganization of parental responsibilities and roles is required. The couple also need to work on reestablishing intimacy. Despite some limitations which warrant attention, these results have important implications for research, given the lack of studies in this area in Portugal, and for clinical practice, since they offer pertinent clues regarding prevention and intervention within this type of family.