Background Non-specific low back pain (NSLBP) is the most prevalent musculoskeletal condition in western countries and is associated with persistent disability and high consumption of health care resources. NSLBP patients first seek primary health care services but the outcomes are often uncertain. This study aimed to examine the clinical course of the outcomes and to identify prognostic indicators for poor outcomes in NSLBP patients who consulted primary care. Methods A prospective cohort study of 115 patients seeking treatment for NSLBP in primary care was conducted. Participants were consecutively recruited by their General Practitioners (GPs) and then assessed at baseline and 2 and 6 months later. Baseline assessment included socio-demographic and clinical data, psychosocial factors, pain, disability, and health related quality of life (HRQoL). Pain, disability, HRQoL and global perception of change were also assessed at 2 and 6-months’ follow-up. In addition, information regarding the GP’ practice was collected. Poor outcomes were determined according to the cut-off point used to define a persistent disabling condition and the minimal important change established for disability, pain and for global perception of change. The relationship between variables on baseline and poor outcomes was modulated through binary logistic regression analysis. The significance of associations was evaluated at ≤ 0.05 p-value with 95% confidence intervals (CI) and adjusted odds ratios (AOR). Results 110 (94.8%) and 104 (89.7%) participants completed the follow-up assessment at 2 and 6 months, respectively. The mean age (±SD) was 48.06 ± 11.41, with 53.9%, (N = 62) reporting an acute presentation of NSLBP. Six months after GP consultation, 53.8% (N = 56) of the participants reported a persistent disabling condition. An “LBP episode of less than 12 weeks” [AOR: 0.26; 95% CI (0.10, 0.65); AOR: 0.34; 95% CI (0.14, 0.81); AOR: 0.21; 95% CI (0.09, 0.53)],”maladaptive psychosocial factors” [AOR: 2.06; 95% CI (1.40, 3.04); AOR: 1.82; 95% CI (1.27, 2.59); AOR: 1.72; 95% CI (1.20, 2.47)] were significantly associated with poor outcomes on disability, pain and global perception of change, respectively. Besides these factors, being employed reduces the chances of poor outcomes on disability [AOR 0.31; 95% CI (0.11, 0.92)]. Conclusions A large proportion of LBP patients seeking primary health care reported poor outcomes 6 months after GP consultation. Patients who report chronic LBP, maladaptive psychosocial factors and are unemployed have a significant increase in the risk of poor outcome. These findings suggest the need of implementing effective models of care able to provide early screening and appropriate treatment to those at greatest risk of a poor outcome.