Visible–near infrared–shortwave infrared (VNIR–SWIR) spectroscopy is being increasingly used for soil organic carbon (SOC) assessment. Common practice consists of scanning soil samples using a single spectrometer. Considerations have rarely been documented of the effects of using multiple instruments and scanning conditions on SOC model calibration that occur when merging soil spectral libraries (SSLs), particularly in soils with low SOC concentration and using both field spectroradiometers and laboratory fixed spectrometers. To address this gap, we scanned 143 low-SOC-content soil samples using three spectrometers (ASD FieldSpec 3, ASD FieldSpec 4, and FOSS XDS) and four setup features - FOSS, contact probe (CP), dark-box (DB), and open laboratory (LAB) - at three laboratories. The application of an internal soil standard (ISS) to align one laboratory spectrum with another for spectral correction and spectral merging of various SSLs was examined. SOC models were developed using i) data from each single spectrometer – single laboratory separately and ii) merged data from multiple spectrometers – different laboratories, applying the 1st derivatives of spectra and random forest (RF) regression. The results indicate that the spectral shape and wavelength position of key features obtained from all spectrometers and setups did not show any noticeable differences, though spectra based on FOSS setup, particularly on low-SOC samples, demonstrated greater range in absolute derivative values regardless of ISS application. The derivative ISS-corrected spectra showed less variation among different spectrometers compared to their uncorrected raw reflectance spectra. All single spectrometer models predicted SOC reasonably well. However, the spectra acquired by the FOSS setup predicted SOC more accurately (R2 = 0.77, RPIQ = 3.30, RMSE = 0.22 %, and SD = 0.04) than the spectra acquired by the other setups. The models derived from merged uncorrected raw reflectance spectra yielded poor results (R2 = 0.48, RPIQ = 2.33, RMSE = 0.33 %, and SD = 0.10); nevertheless, assessment of SOC using the 1st derivative ISS-corrected merged SSLs considerably improved the prediction accuracy (R2 = 0.70, RPIQ = 3.10, RMSE = 0.25 %, and SD = 0.06). Hence, the derivative spectra coupled with the ISS correction improved the accuracy of SOC prediction models obtained from the merged soil spectra collected in different environments using different instruments. We therefore recommend application of the ISS spectral alignment method linked to the 1st derivative approach to enhance the compilation of SSLs at the regional and global scales for SOC assessment.