We report the fabrication of a low-cost paper-based SERS platform with enhanced sensing capabilities. The sensor consists of a highly concentrated glycerol/ethanol dispersion of ca. 77 nm Au nanospheres (AuSph) inkjet-printed on hydrophobic chromatographic paper forming circular sensing spots of 1 mm in diameter. The AuSph ink exhibits high stability for 1 year. Interestingly, we demonstrate that the modification of the paper surface with hydrophobic ligands improve the sensing capabilities by confining the analyte solution in the AuSph sensing platform. It contributes to both concentrate the analyte, as well as, to decrease the sample volume to just a few μl. We also analyze the effect of the amount of the nanoparticles, tunable by the number of printing cycles, in the SERS performance of the plasmonic spots. The results show that 5 printing cycles give rise to sensing platforms with great SERS response in terms of intensity and uniformity. The spot-to-spot reproducibility is also analyzed observing good results even for AuSph spots from different printed papers. The paper-based SERS platform was tested towards the detection of crystal violet (CV) and the fungicide thiram. Additionally, applying a digital protocol for SERS analysis, a good linear correlation between the digital counts (or positive events) and the analyte concentration was obtained at the single-molecule SERS regime. In both cases, the quantification region threshold was 10−11 M. The great sensitivity performance of the inkjet-printed SERS substrate is reflected by the low sample volume needed (only 2 μL). The inkjet-printed SERS substrate and the fabrication method demonstrated to be efficient, reliable, reproducible and robust, with a cost less than $ 0.01 per spot.