A new method to stabilize and functionalize surfaces for surface-enhanced Raman spectroscopy (SERS) is demonstrated. Atomic layer deposition (ALD) is used to deposit a sub-1-nm alumina layer on silver film-over-nanosphere (AgFON) substrates. The resulting overlayer maintains and stabilizes the SERS activity of the underlying silver while presenting the surface chemistry of the alumina overlayer, a commonly used polar adsorbent in chromatographic separations. The relative affinity of analytes for alumina-modified AgFON substrates can be determined by their polarity. On the basis of SERS measurements, dipicolinic acid displays the strongest binding to the ALD alumina-modified AgFON among a set of pyridine derivatives with varying polarity. This strong affinity for carboxylate groups makes the SERS substrate an ideal candidate for bacillus spores detection using the dipicolinate biomarker. The SERS signal from extracted dipicolinate was measured over the spore concentration range 10(-14)-10(-12) M to determine the saturation binding capacity of the alumina-modified AgFON surface. The adsorption constant was determined to be K-spore = 9.0 x 10(13) M-1. A 10-s data collection time is capable of achieving a limit of detection of similar to 1.4 x 10(3) spores. The shelf life of prefabricated substrates is at least 9 months prior to use. In comparison to the bare AgFON substrates, the ALD-modified AgFON substrates demonstrate twice the sensitivity with 6 times shorter data acquisition time and 7 times longer temporal stability. ALD expands the palette of available chemical methods to functionalize SERS substrates, which will enable improved and diverse chemical control over the nature of analyte-surface binding for biomedical, homeland security, and environmental applications.