Actinic keratoses (AKs) can progress into invasive squamous cell carcinoma and thus may become a life threatening disease. Argon plasma coagulation (APC) might complement the therapeutic armamentarium in particular for AK lesions. However, there is no data on APC-induced micromorphological changes following the treatment of AKs. We aimed to determine in vivo APC-induced effects on the epidermis and dermoepidermal junction (DEJ) zone in AK lesions. We performed APC in 108 AKs using the spray mode with a power setting of 15 W and a flow rate of 2.0 L/min. Before and after the intervention, optical coherence tomography (OCT) was performed. After APC, 74.2% (46/62) lesions presented with clearly demarcated DEJ and without any epidermal tissue left, 25.8% (16/62) of treated lesions showed residual epidermal tissue left. In 19.4% (12/62), parts of the DEJ and in 6.5% (4/62), the entire DEJ could not be discriminated. The χ test showed a significant (P = 0.0025) association between the presence of hyperkeratosis prior to APC and intact DEJ after APC. In conclusion, APC as shown by OCT is a well controllable treatment modality for AKs causing only limited damage to dermal tissue. Further studies are needed to evaluate clinical outcome as well as recurrence rates.