Abstract Background Guidelines are often slowly adapted into clinical practice. However, actively supporting healthcare professionals in evidence-based treatment may speed up guideline implementation. Danish low back pain (LBP) guidelines focus on primary care treatment of LBP, to reduce referrals from primary care to secondary care. The primary aim of this project was to reduce secondary care referral within 12 weeks by a multifaceted implementation strategy (MuIS). Methods In a cluster randomised design, 189 general practices from the North Denmark Region were invited to participate. Practices were randomised (1:1) and stratified by practice size to MuIS (28 practices) or a passive implementation strategy (PaIS; 32 practices). Included were patients with LBP aged 18 to 65 years who were able to complete questionnaires, had no serious underlying pathology, and were not pregnant. We developed a MuIS including outreach visits, quality reports, and the STarT Back Tool for subgrouping patients with LBP. Both groups were offered the usual dissemination of guidelines, guideline-concordant structuring of the medical record, and a new referral opportunity for patients with psycho-social problems. In an intention-to-treat analysis, the primary and secondary outcomes pertained to the patient, and a cost-effectiveness analysis was performed from a healthcare sector perspective. Patients and the assessment of outcomes were blinded. Practices and caregivers delivering the interventions were not blinded. Results Between January 2013 and July 2014, 60 practices were included, of which 54 practices (28 MuIS, 26 PaIS) included 1101 patients (539 MuIS, 562 PaIS). Follow-up data for the primary outcome were available on 100 % of these patients. Twenty-seven patients (5.0 %) in the MuIS group were referred to secondary care vs. 59 patients (10.5 %) in the PaIS group. The adjusted odds ratio (AOR) was 0.52 [95 % CI 0.30 to 0.90; p = 0.020]. The MuIS was cost-saving £−93.20 (£406.51 vs. £499.71 per patient) after 12 weeks. Conversely, the MuIS resulted in less satisfied patients after 52 weeks (AOR 0.50 [95 % CI 0.31 to 0.81; p = 0.004]). Conclusions Using a MuIS changed general practice referral behaviour and was cost effective, but patients in the MuIS group were less satisfied. This study supports the application of a MuIS when implementing guidelines. Trial registration ClinicalTrials.gov, NCT01699256