Background – A number of German statutory health insurance companies are offering integrated care contracts for homeopathy (ICCHs) that cover the reimbursement of homeopathic treatment. The effectiveness and cost-effectiveness of these contracts are highly debated. Methods – To evaluate the effectiveness and cost-effectiveness of treatment after an additional enrollment in an ICCH, a comparative, prospective, observational study was conducted in which participants in the ICCH (HOM group) were compared with matched (on diagnosis, sex and age) insured individuals (CON group) who received usual care alone. Those insured with either migraine or headache, allergic rhinitis, asthma, atopic dermatitis and depression were included. Primary effectiveness outcomes were the baseline adjusted scores of diagnosis-specific questionnaires (e.g. RQLQ, AQLQ, DLQI, BDI-II) after 6 months. Primary cost-effectiveness endpoints were the baseline adjusted total costs from an insurer perspective in relation to the achieved quality-adjusted life years (QALYs). Costs were derived from health claims data and QALYs were calculated based on SF-12 data. Results – Data from 2524 participants (1543 HOM group) were analyzed. The primary effectiveness outcomes after six months were statistically significant in favor of the HOM group for migraine or headache (Δ = difference between groups, days with headache: − 0.9, p = 0.042), asthma (Δ-AQLQ(S): + 0.4, p = 0.014), atopic dermatitis (Δ-DLQI: − 5.6, p ≤ 0.001) and depression (Δ-BDI-II: − 5.6, p ≤ 0.001). BDI-II differences reached the minimal clinically important difference. For all diagnoses, the adjusted mean total costs over 12 months were higher in the HOM group from an insurer perspective, with migraine or headache, atopic dermatitis and depression suggesting cost-effectiveness in terms of additional costs per QALY gained. Conclusion – After an additional enrollment in the ICCH, the treatment of participants with depression showed minimally clinically relevant improvements. From an insurer perspective, treatment with an ICCH enrollment resulted in higher costs over all diagnoses but seemed to be cost-effective for migraine or headache, atopic dermatitis and depression according to international used threshold values. Based on the study design and further limitations, our findings should be considered cautiously and no conclusions regarding the effectiveness of specific treatment components can be made. Further research is needed to overcome limitations of this study and to confirm our findings.