This study examined the physiological and biochemical effects of pulsed acoustic stimulation on Kalanchoe pinnata (Crassulaceae) under controlled environmental conditions. The objective was to determine whether sinusoidal sound waves could influence seed germination, vegetative growth, and the accumulation of methanol-extractable secondary metabolites, referred to here as secondary methanoliths. The experiment was conducted in a 40 × 20 cm mini greenhouse maintained at 25 ± 2 °C, 60–70% relative humidity, and a 12 h light/12 h dark cycle. A Raspberry Pi minicomputer running Pure Data software generated sinusoidal waves in the 3–5 kHz range, amplitude-modulated at 615 Hz, and delivered for one hour daily (06:00–07:00) at 85 ± 5 dB. Quantitative assessment revealed that acoustic stimulation significantly enhanced germination, with 92% of seeds showing radicle emergence after seven days compared with 80% in controls. Vegetative parameters also improved: stem elongation increased by 16%, leaf number by 12%, and total fresh biomass by nearly 15%. High-performance liquid chromatography coupled with mass spectrometry (HPLC–MS) analysis showed a 33% rise in methanol-extractable secondary metabolites, particularly bufadienolides and flavonoid derivatives. Morphological observations confirmed that treated plants exhibited more vigorous and uniform development without signs of mechanical stress or deformation. These results demonstrate that precisely modulated high-frequency sound acts as a beneficial physical stimulus capable of enhancing both primary and secondary metabolism in K. pinnata. The combined effects on germination, growth, and metabolite production suggest activation of mechanosensitive signaling pathways, possibly involving calcium influx and jasmonate-related responses. This work supports the concept that acoustic energy can be harnessed as a sustainable, non-chemical strategy to optimize the productivity and phytochemical potential of medicinal and ornamental plants.