This study aimed to assess the effects of pecan and mesquite wood, as well as smoking time, on anthraquinone (AQ) levels and quality properties of chipotle pepper (CHP) during the traditional smoking process. Changes in moisture content, microstructure, levels of total phenols (TPs), AQ, capsaicin (CAPS), dihydrocapsaicin (DHC), total polyphenols (TPPs), and total antioxidant activity (TAA), as well as color parameters, were measured. A wood mixture consisting of pecan, poplar, mesquite, and pine was used as the control. The CHP moisture content consistently decreased from 12 to 108 h of smoking, with long times exhibiting asymptotic trends across all treatments. Concurrently, structural changes, such as pericarp thinning and plant tissue collapse, were observed as the smoking process progressed. The wood type and processing time had a significant impact (P < 0.05) on TPs, AQ, CAPS, DHC, TAA levels, and color. TPs and AQ exhibited behavior opposite to that of the moisture content. CHP smoked in mesquite wood exhibited the highest TPs absorption rate and the lowest AQ levels. However, the AQ levels in CHP using any wood type exceeded permissible limits (0.02 mg·kg−1) at 12 h of processing, with the control exhibiting the highest AQ concentrations. The highest concentrations of CAPS and DHC were observed at 36 h in all treatments, with lower losses in mesquite wood CHP. The control exhibited the highest TAA values compared to fresh peppers. CHP color (a*, redness) decreased throughout the smoking process. The pecan and mesquite wood treatments resulted in the lowest loss of a* (P < 0.05). These results indicate that using mesquite wood for CHP production promotes higher TPs concentrations with lower AQ levels, followed by pecan wood, when compared to the control. These findings suggest the need to investigate the mechanisms of AQ formation to achieve CHP parameters within the regulatory limits with good quality.