The COVID-19 pandemic and the ongoing lockdowns might have had a strong impact on mental health of mothers and their infants/toddlers. For example, families had to deal with health issues and social isolation, which might have affected mental health and parent-child interactions. The aim of this study is to evaluate differences in (1) infantile regulatory disorders, (2) maternal mental health, (3) the impact of maternal mental health on infantile regulatory disorders, and (4) alterations in the mother-child interaction for participants recruited before versus after the onset of the first German lockdown. For this reason, mother-child dyads have been divided into two groups and were compared by analyzing clinical interviews on psychopathology of mother and child (M.I.N.I. & DC:05) and mother-child-interactions (Emotional Availability Scales). Results showed that (1) differences in infantile sleeping disorders emerged (phi = 0.243; p = 0.016) compared to the pre-lockdown group, while (2) the occurrence of maternal panic and anxiety increased in the post-lockdown group (phi = 0.229; p = 0.022). Moreover, there was (3) an association for maternal panic and child’s sleep disorder, and (4) specific associations with maternal non-hostility in the mother-child-interaction. In conclusion, the present study highlights the differences of maternal mental health occurrences and infants’ regulatory problems, as well as the possible effects of the COVID-19 pandemic for infants. In the pre-lockdown group, maternal non-hostility might have acted as a promotive factor against regulatory disorders, while this mechanism was mitigated in the post-lockdown group.