Abstract Background Psychotherapy of mother-child dyads is an intervention which was developed to prevent maltreatment and negative children’s development. There is a lack of good-quality research investigating psychotherapeutic interventions and social care for mothers at high-risk living in Mother-Child Facilities in Germany. The present randomized controlled pilot trial (RCT) aimed to evaluate the need for parent-infant psychotherapy (PIP) and to explore its impact on the mother-infant relationship. Primary feasibility objectives were recruitment and attrition, with potential efficacy defined as the secondary feasibility objective. Methods This pilot RCT focused on (young) mothers with cumulative risk factors and their infants under 7 months of age living in Mother-Child Facilities. N=32 mother-child dyads were randomly allocated to PIP or Care as usual (CAU). Outcomes were assessed at baseline, 3 months, and 6 months of intervention. The primary potential efficacy outcome was maternal sensitivity. Secondary outcomes were maternal mental health problems, reflective functioning, parenting stress, personality organization, infant’s development, and attachment. Results At baseline, all mothers showed low levels of emotional availability, but results revealed improvements in sensitivity, mental health problems, stress, and depressive symptomatology favoring PIP after 6 months. Positive developments in maternal sensitivity, a healthy aspect of mother-child interaction, were only found in the PIP group. Overall attrition was high at 6 months. Some evidence of fewer depressive symptoms and lower maternal distress after 6 months of PIP-intervention exists that did not reach significance. Conclusion Findings revealed improvements in the mother’s well-being for both groups, but PIP had a higher impact on the mother-child dyad. In sum, there is some evidence that PIP may represent an effective intervention offer besides the social and pedagogical support in these facilities, but further research is demanded. Trial registration DRKS00022485 (retrospectively registered).