Background: People with multimorbidity, defined as the co-existence of two or more chronic conditions in an individual, often suffer from pain and functional limitations caused by musculoskeletal disorders and the chronic conditions. In chiropractic practice, two thirds of patients are treated for low back pain (LBP). It is unknown to what extent LBP is accompanied with chronic conditions in chiropractic practice. The objective was to determine the prevalence of multimorbidity among patients with LBP in chiropractric practice and to investigate if multimorbidity affects pain intensity, self-rated health, physical and mental health. Finally, to explore if individuals with multimorbidity have a different recovery for the LBP. Methods: Patients presenting with a new episode of LBP were recruited from 10 chiropractic clinics in 2016–2018. Patient-reported data concerning socio-demographics, self-rated health, pain intensity, history of LBP, mental health and chronic conditions were collected at baseline. The prevalence of multimorbidity was determined. To evaluate differences in recovery from the LBP, we estimated changes in the Roland Morris Disability Questionnaire (RMDQ) score and use of pain medication at baseline, 2 weeks, 3 months and 12 months. The analyses were adjusted using regression models. Results: 2083 patients were included at baseline and 71%, 68% and 64% responded to follow-up questionnaires at 2 weeks, 3 and 12 months. 1024 (49%) participants reported to have at least one chronic condition and 421 (20%) had multimorbidity (≥ 2 chronic conditions). The presence of multimorbidity was associated with increased odds of poor self-rated health (OR 2.13), physical fitness (OR 1.79), poor muscular strength (OR 1.52), poor endurance (OR 1.51), and poor balance (OR 1.33). Patients with high LBP intensity combined with multimorbidity showed a poorer recovery than patients without chronic diseases (mean difference in RMDQ score 3.53 at 12 months follow-up). More patients with multimorbidity used pain medication for LBP at 12 months follow-up compared to those without chronic disease (OR 2.36). Conclusions: Chiropractors should be aware that patients with LBP may suffer from multimorbidity with poor general health. Patients with multimorbidity also have poorer recovery from LBP than people without chronic disease and clinical follow-up may be indicated.