There is a positive association between bacteraemia with Streptococcus bovis–Streptococcus equinus complex (SBSEC) and colorectal cancer (CRC). However, the relationship between the timing of SBSEC bacteraemia and CRC is not well-established. Associations with other gastrointestinal cancers have also been suggested. Using national registries, we retrospectively examined the incidence of CRC and other gastrointestinal cancers after SBSEC-bacteraemia in Sweden 2010–2019, and analysed the timing, characteristics, and prognosis of diagnosed CRC. Individuals with SBSEC-bacteraemia were matched to randomly selected controls from the general population at a 1:10 ratio. Cox-regression determined CRC hazard ratios (HR). In total, 908 individuals with SBSEC-bacteraemia were identified and 9,080 controls, of whom 75/908 (8.3%) and 168/9080 (1.9%) respectively had previously diagnosed CRC (p < 0.01). During follow-up of individuals without previous CRC, CRC was diagnosed in 45/833 (5.4%) individuals with SBSEC and 114/8912 (1.3%) controls (p < 0.01). The HR of CRC diagnosis for SBSEC was 10.3 (95% CI 6.7–15.8) overall and 19.8 (95% CI 11.1–35.3) during the first year of follow-up. In conclusion, there was an increased incidence of CRC, and most were diagnosed within the first year. Neither the tumour location, −stage, or -grade of diagnosed CRC nor the rates of other gastrointestinal cancers differed significantly.