Background Thoracodorsal artery perforator (TDAP) flap and muscle‐sparing latissimus dorsi (MSLD) flap have been frequently used for axillary coverage after hidradenitis suppurativa (HS) excision. However, none showed superiority to others. This study compared both flaps to define the ideal option, highlighting flap outcomes and functional and aesthetic results. Methods A retrospective study was conducted to compare both flaps that were used for axillary reconstruction in nine patients with bilateral HS Hurley stage III between 2017 and 2020. Eight TDAP and 10 MSLD flaps underwent functional evaluation using shoulder abduction angle (SA); the Disabilities of the Arm, Shoulder, and Hand (DASH) score; visual analog scale (VAS) for pain; and the Dermatology Life Quality Index (DLQI) questionnaires. Aesthetic assessment included the Scar Cosmesis Assessment and Rating (SCAR) scale and arm–chest interval. Results The mean operating time was 194.4 ± 51.58 and 128.5 ± 31.45 min for TDAP and MSLD (p = .009), respectively. Flap complications were significantly higher in the TDAP group (p = .034). There was no significant difference between both groups regarding SA; DASH, DLQI, VAS, and SCAR scale (p > .05). The mean arm–chest interval was significantly longer in the MSLD than in the TDAP group by 6.9 mm (p = .001). Conclusions TDAP and MSLD are comparable versatile flaps to eradicate axillary HS with higher TDAP flap complications. Although the TDAP flap is less bulky than the MSLD flap, the MSLD flap shortens the harvesting time without a significant difference in functional outcomes and scar results.