There is increasing evidence that diversity changes in bacterial communities of beef cattle correlates to the presence of Shiga toxin-producing Escherichia coli (STEC). However, studies that found an association between STEC and bacterial diversity have been focused on pre-slaughter stages in the beef supply chain. This study was designed to test a hypothesis that there is no differences in bacterial diversity between samples with and without the presence of Top 7 STEC (O26, O45, O103, O111, O121, O145 and O157) throughout processing in an integrated (abattoir A) and a fragmented (abattoir B) Australian beef abattoir. Slaughter and boning room surface samples from each abattoir were analysed using 16S rRNA amplicon sequencing and tested for Top 7 STEC following the Food Safety Inspection Services protocol. Potential positives (PPs) through slaughter were similar between the abattoirs (64 – 81%). However, abattoir B had substantially reduced PPs in the boning room compared to abattoir A (A: 23% and 48%, B: 2% and 7%). Alpha diversity between the sample groups was not significantly different (P>0.05) regardless of different STEC markers. Non-metric multidimensional scaling (nMDS) of slaughter samples showed that the bacterial composition in faecal and hide samples shared the least similarity with the communities in carcase and environmental samples. Surface samples from slaughter (carcase and environmental) and boning (carcase, beef trim and environmental) all appeared randomly plotted on nMDS. This indicated that the STEC presence also did not have a significant effect (P>0.05) on beta diversity. While presence of STEC appeared to correlate with changes in diversity of faecal and hide bacterial communities in previous studies, it did not appear to have the same effect on other samples throughout processing.