Methicillin-resistant Staphylococcus aureus (MRSA) infections contribute significantly to the mortality rate associated with antimicrobial resistance, while also increasing medical complications when compared to methicillin-sensitive isolates. Consequently, increasing the efficacy of β-lactams may alleviate the burden associated with this drug–pathogen combination. Dialysed extracts, derived from Pelvetia canaliculata, were further partitioned to generate phlorotannin enriched extracts (PEEs). Minimum inhibitory concentrations (MICs) of extracts were used to determine the antimicrobial and antibiotic-modulating activity against seven clinical MRSA isolates. Whole-transcriptomic sequencing was carried out to determine potential mechanisms of action on the strongest extract–antibiotic combination against an MRSA isolate, determined by the fractional inhibitory concentration index (FICI). The most pronounced β-lactam modulatory effects were seen in the >100 kDa PEE from P. canaliculata in conjunction with amoxicillin (MIC fold-reductions = 12.8–214), while >30 kDa PEE resulted in the strongest FIC index value when combined with penicillin (0.23), indicating a synergistic effect. Whole-transcriptome analysis of this treatment identified multiple differentially expressed genes (Log2FC +1/−1) of statistical significance (p adj < 0.05), namely related to accelerated autolysis, cell-envelope stability, protein synthesis, DNA replication, iron homeostasis and active transport. This study highlights preliminary transcriptomic evidence of biological processes associated with penicillin modulation by P. canaliculata > 30 kDa PEE, providing a foundation for further investigation of its antibiotic-modulating activity.