The objective of this study was to evaluate whether clinical factors at baseline in patients with non-specific neck pain are related to recovery after treatment with manual therapy versus physiotherapy. Participating physiotherapists recruited new consulters with complaints of the neck and/or upper extremity. For this study we selected patients from this cohort with non-specific neck complaints. Participants filled in questionnaires at baseline, 3 and 6 months. The main outcome measure was recovery at 6 months follow-up. Possible predictors like complaint-specific factors, physical factors, social and psychological factors were evaluated for interaction with treatment. Of the 396 participants in this study, 97 (24.5%) received manual therapy, all others received physiotherapy, consisting of exercises, massage or physical applications. In the multivariable model four variables were significantly related to recovery: duration of complaint, catastrophising, distress and somatisation. Severity of main complaint and catastrophising appeared to show interaction with treatment. It appeared that every point increase in severity or catastrophising resulted in a lower chance to recover from physiotherapy compared to manual therapy. In conclusion, severity of main complaint and catastrophising seem to modify treatment success. Increased pain severity or catastrophising at baseline increased the chance of treatment success after manual therapy compared to physiotherapy.