Background: Models of collaborative care and consultation liaison propose organizational changes to improve the quality of care for people with common mental disorders, such as anxiety and depression. Some literature suggests only short-term positive effects of consultation liaison on patient-related outcomes, whereas collaborative care demonstrates both short-term and long-term positive effects. To our knowledge, only one randomized trial has compared the effects of these models. Collaborative care was superior to consultation liaison in reducing symptoms of depression for up to 3 months, but the authors found no difference at 9-months' follow-up. The Collabri Flex Trial for Depression and the Collabri Flex Trial for Anxiety aim to compare the effects of collaborative care with those of a form of consultation liaison that contains potential contaminating elements from collaborative care. The trials build on knowledge from the previous cluster-randomized Collabri trials. Methods: Two randomized, investigator-initiated, parallel-group, superiority trials have been established: one investigating the effects of collaborative care vs consultation liaison for depression and one investigating the effects of collaborative care vs consultation liaison for generalized anxiety, panic disorder and social anxiety disorder at 6-months' follow-up. Participants are recruited from general practices in the Capital Region of Denmark: 240 in the depression trial and 284 in the anxiety trial. The primary outcome is self-reported depression symptoms (Beck Depression Inventory (BDI-II)) in the depression trial and self-reported anxiety symptoms (Beck Anxiety Inventory (BAI)) in the anxiety trial. In both trials, the self-reported secondary outcomes are general psychological problems and symptoms (Symptom Checklist 90-Revised), functional impairment (Sheehan Disability Scale) and general well-being (World Health Organization-Five Well-Being Index). In the depression trial, BAI is an additional secondary outcome, and BDI-II is an additional secondary outcome in the anxiety trial. Explorative outcomes will also be collected. Discussion: The results will supplement those of the cluster-randomized Collabri trials and provide pivotal information about the effects of collaborative care in Denmark. Trial registration: ClinicalTrials.gov, NCT03113175 and NCT03113201. Registered on 13 April 2017.