Anal fistulas often cause significant impairment to patients' health-related quality of life (HRQOL). This cross-sectional study aimed to compare the HRQOL between patients with anal fistulas with inflammatory bowel disease (IBD) and those without, hypothesizing significant differences in HRQOL scores between these groups. The secondary objectives were to identify specific aspects of life quality most affected and explore potential variables influencing HRQOL. The study was conducted at the Clinical Emergency Hospital "Pius Brinzeu" in Timisoara, Romania, using a convenience sample of 175 adult patients diagnosed with anal fistulas, stratified into IBD and non-IBD groups. Quality of life was evaluated at initial hospital admission and three months post-treatment using four questionnaires: SF-36, GIQLI, HADS, and the WHOQOL-BREF. Initial SF-36 scores were marginally lower in the IBD group, with mean physical and mental scores of 52.0 and 54.5, respectively. Both groups showed an improvement after intervention, but the mean difference was higher in the IBD group, with an increase of 1.1 in physical score. Initial GIQLI scores were significantly lower in the IBD group (110) compared to the non-IBD group (116). Post-intervention, the mean scores increased to 116 and 121, respectively. HADS scores suggested higher anxiety levels in the non-IBD group (7.5 vs. 6.1), although depression scores were similar. Post-intervention, anxiety scores decreased more substantially in the non-IBD group (-0.9 vs. -0.3). The WHOQOL-BREF scores were lower across all domains for the IBD group at the initial test (physical health: 12.4, psychological health: 14.9, social relationships: 14.4, environment: 13.0). Post-intervention, scores increased marginally in the IBD group (physical health: 12.7, psychological health: 15.9, social relationships: 14.1, environment: 13.8) but varied in the non-IBD group. HRQOL, as measured by multiple questionnaires, is impacted differently in anal fistula patients with and without IBD. These findings highlight the importance of a tailored approach to managing this patient population to improve their quality of life post-treatment.