A high-throughput abbreviated liquid chromatography mass spectrometric (ACMS) method was used to assess the relative influence of genotype and temperature on polyphenol composition in cloudberries. Principal component analysis (PCA) plots of the collated ACMS data showed a separation between crosses based on their female parents (Nyby or Fjellgull). Crosses with Nyby as the female parent had higher relative levels of masses assignable to certain ellagitannin derivatives. Crosses with Fjellgull had higher levels of distinctive masses assignable to quercetin derivatives (including a hydroxy-3-methylglutaroyl hexose derivative not previously identified in cloudberry) and anthocyanin derivatives. There was also a separation between samples grown at lower and higher temperatures, which was driven by m/z signals associated with ellagitannins and notably a major component, sanguiin H-6. Therefore, abbreviated MS techniques can discern genetic and/or environmental influences in polyphenol composition and can quickly assess quality in breeding programmes or in response to environmental changes.