Background: Acne conglobata (AC) and nodulocystic acne have long been confused clinically, despite the presentation and the response to treatment being different. AC and hidradenitis suppurativa (HS) resemble each other; a subtype of HS called “conglobata phenotype” has recently been reported in a large Dutch cohort. Acne vulgaris and HS are often associated. Isotretinoin is typically ineffective in treating HS and may even aggravate it, but it is often indispensable in treating acne vulgaris. Objective: The aim of the study was to assess whether isotretinoin may be used safely in adults with both HS and acne vulgaris and when it might be contraindicated. Materials and Methods: Belgian HS patients from the European Registry for Hidradenitis Suppurativa Registry (ERHS) reporting a history of severe acne of the face and/or the back, and who have ever used isotretinoin for their acne, were all selected. Patients whose acne worsened on isotretinoin were compared to patients whose acne did not worsen (improvement or no change). Results: Among the 82 selected patients, 10 (12.2%) report that their acne was aggravated while taking isotretinoin, while 72 (87.8%) report that their acne was not aggravated on isotretinoin. Of the 10 HS patients whose acne worsened with isotretinoin, 9 (90%) were men (p = 0.04) and 8 (80%) were HS “conglobata phenotype” (p < 0.001). In contrast, 47 (65.3%) of the 72 patients whose acne did not worsen on isotretinoin belonged to the HS “regular phenotype” (p = 0.01). On multivariate analysis, the item most strongly associated with poor response to isotretinoin was the HS “conglobata phenotype,” followed by body mass index (BMI) (worse response to isotretinoin if BMI >25 kg/m2). Additionally, of 26 patients who received isotretinoin while their HS had already started, only 6 (23.1%) reported isotretinoin effectiveness on their HS. Conclusion: Subject to confirmation by larger studies, our study suggests that isotretinoin should be avoided in the treatment of acne in HS patients with the HS “conglobata phenotype,” as it may worsen the acne, likewise being male or having a BMI above 25 seems to increase this risk of a bad therapeutic outcome. Patients with an HS “regular phenotype” appear to be at a reduced risk of isotretinoin treatment worsening their acne.