A well-implemented Earthquake Early Warning (EEW) system can warn populations about imminent shaking due to earthquakes. The Canadian EEW network covers regions where there is high seismic hazard and dense population, and where critical infrastructure is located. Within these coverage areas, some of the newly deployed EEW stations are located on soft soil and sediment, which can cause deviations from predicted ground motion due to site amplification effects. This contrasts with the current Canadian National Seismic Network (CNSN) stations primarily located on bedrock. The goal of this study is to provide empirical site amplification factors that reflect deviations between predicted ground motion and measured ground motion at EEW sites. We calculate the horizontal-to-vertical spectral ratios (HVSRs) at each EEW site using ambient seismic noise and estimate the predominant site period using a systematic Gaussian curve-fitting algorithm. From a total of 75 Canadian EEW stations investigated, 26% show site amplification compared to 6% of CNSN sites. We have assessed the relationship between the existing catalogue of CNSN station magnitude residuals, predominant site period, and amplification at the site. While station magnitude residuals are used to estimate site-specific amplification at CNSN stations, EEW stations do not contribute to the Canadian National Earthquake Database (NEDB) magnitude estimates. Therefore the HVSR ambient noise method is used for site-specific amplification estimates at these stations. Our comparative analysis characterizes the relationship between EEW and NEDB magnitudes in western and eastern Canada and describes how the application of site amplification factors can improve EEW magnitude estimates.