Introduction Acetylcholinesterase (AChE) inhibitors are considered an important strategy in the treatment of neurological disorders such as Alzheimer's disease. A simple and fast planar chromatography‐bioassay methodology has been established to detect bioactive molecules in cherimoya fruit. Objective Detect and identify AChE inhibitors in cherimoya by high‐performance thin‐layer chromatography (HPTLC)‐bioassay‐mass spectrometry (MS) and related techniques. Methodology Effect‐directed analysis by planar chromatography‐bioassay‐mass spectrometry was applied to detect and identify AChE inhibitors in pulp, peel and cherimoya seed. Bioassay was optimised establishing the following conditions: enzymatic solution (1.0 U mL−1), 1‐naphtyl acetate substrate (1.5 mg mL−1) and Fast Blue B salt (1.0 mg mL−1). TLC‐MS interface was used to directly elute the active zones into a mass spectrometer or to a micro‐vial for further off‐line studies. Results Two AChE inhibitory bands were detected in peel extracts. An analysis via HPTLC‐MS and high‐performance liquid chromatography diode array detector tandem mass spectrometry (HPLC‐DAD‐MS/MS) allowed to characterise three potential AChE inhibitors: anonaine (m/z 266 [M + H]+; UV λmax = 269.6 nm), glaucine (m/z 256 [M + H]+; UV λmax = 282.9 and 300.6 nm) and xylopine (m/z 296 [M + H]+; UV λmax = 278.5 nm). Conclusions The application of this optimised high throughput method allowed to establish the presence of three potential AChE inhibitors in cherimoya peel. For the first time AChE inhibitory capacity of these alkaloids is reported.