(1) Background: Targeted alpha therapy is a new emerging field in nuclear medicine driven by the two advantages of overcoming resistance of cancer-suffering patients against beta therapies and practically application of lower activities of 212Pb- and 225Ac-labelled peptides to reach the same doses compared to beta therapy due to the high cytotoxic nature of alpha particles. Quality control of the 212Pb/225Ac-radiopharmaceuticals remains a challenge due to the low activity levels used for therapy (100 kBq/kg) and the formation of several free daughter nuclides immediately after formulation of patient doses; (2) Methods: The routine alpha detection of thin-layer chromatograms (TLC) of 212Pb- and 225Ac-labelled peptides using a MiniScanPRO+ scanner combined with an alpha detector head was compared with detection using an AR-2000 scanner equipped with an open proportional counter tube. Measurement time, resolution and validity were compared for both scanners; (3) Results: For 225Ac quality control the values of RCP are within the acceptance criteria 2 h after TLC development, regardless of when the TLC probe was taken. If the TLC probe was taken 24 h after radiosynthesis, the true value of RCP within the acceptance criteria was not measured until 5 h after TLC development. For 212Pb-labelled peptides, the probe sampling did not have a high impact on the value of RCP for the MiniScanPRO+ and AR-2000. A difference was observed when measuring the TLC with the AR-2000 in different modes; (4) Conclusions: The MiniScanPRO+ is fast, does not require additional equipment and can also measure the gamma spectrum, which may be important for some radiopharmaceutical production sites and regulatory authorities. The AR-2000 has a better signal-to-noise ratio and this eliminates the need for additional waiting time after TLC development.