Psychobiological responses to music have been examined previously in various naturalistic settings in adults. Choir singing seems to be associated with positive psychobiological outcomes in adults. However, evidence on the effectiveness of singing in children and adolescents is sparse. The COVID-19 outbreak is significantly affecting society now and in the future, including how individuals engage with music. The COVID-19 pandemic is occurring at a time when virtual participation in musical experiences such as singing in a virtual choir has become more prevalent. However, it remains unclear whether virtual singing leads to different responses in comparison with in-person singing. We evaluated the psychobiological effects of in-person choral singing (7 weeks, from January to March 2020, before the COVID-19 outbreak) in comparison with the effects of virtual choral singing (7 weeks, from May to July 2020, after schools partly re-opened in Austria) in a naturalistic pilot within-subject study. A group of children and young adolescents (N = 5, age range 10–13, female = 2) from a school in Salzburg, Austria were recruited to take part in the study. Subjective measures (momentary mood, stress) were taken pre- and post-singing sessions once a week. Additionally, salivary biomarkers (cortisol and alpha-amylase) and quantity of social contacts were assessed pre- and post-singing sessions every second week. Psychological stability, self-esteem, emotional competences, and chronic stress levels were measured at the beginning of in-person singing as well as at the beginning and the end of the virtual singing. We observed a positive impact on mood after both in-person and virtual singing. Over time, in-person singing showed a pre-post decrease in salivary cortisol, while virtual singing showed a moderate increase. Moreover, a greater reduction in stress, positive change in calmness, and higher values of social contacts could be observed for the in-person setting compared to the virtual one. In addition, we observed positive changes in psychological stability, maladaptive emotional competences, chronic stress levels, hair cortisol, self-contingency and quality of life. Our preliminary findings suggest that group singing may provide benefits for children and adolescents. In-person singing in particular seems to have a stronger psychobiological effect.