For the first time, electromembrane extraction (EME) combined LC-MS/MS was applied to extract and determine α-solanine and α-chaconine in different potato tissues using NPOE containing 20% (v/v) DEHP as supported liquid membrane (SLM). Under the optimal conditions, the proposed EME-LC-MS/MS method was evaluated using spiked fresh potato peel sample. The linear range for α-solanine and α-chaconine was 5–1000 ng mL⁻¹ (R² > 0.9991), with LOD and LOQ of 1.2–1.5 ng mL⁻¹ and 4.1–5.2 ng mL⁻¹, respectively. Repeatability for α-solanine and α-chaconine at three concentration levels was satisfactory (<4.9%), and recoveries ranged from 73% to 106%. Finally, the EME-LC-MS/MS method has been successfully employed to determine α-solanine and α-chaconine in sprouted potato peel and tuber samples, indicating that EME exhibited high selectivity and efficient sample clean-up capability. Consequently, EME showed great potential for extraction and purification of toxic and bioactive basic compounds from complex plant tissues.