This study aimed to compare different ultrasound devices with magnetic resonance spectroscopy (MRS) to quantify muscle lipid content from echo intensity (EI). Four different ultrasound devices were used to measure muscle EI and subcutaneous fat thickness in four lower-limb muscles. Intramuscular fat (IMF), intramyocellular (IMCL) and extramyocellular lipids (EMCL) were measured using MRS. Linear regression was used to compare raw and subcutaneous fat thickness-corrected EI values to IMCL, EMCL and IMF. IMCL had a poor correlation with muscle EI (r = 0.17–0.32, NS), while EMCL (r = 0.41–0.84, p < 0.05–p < 0.001) and IMF (r = 0.49–0.84, p < 0.01–p < 0.001) had moderate to strong correlation with raw EI. All relationships were improved when considering the effect of subcutaneous fat thickness on muscle EI measurements. The slopes of the relationships were similar across devices, but there were some differences in the y-intercepts when raw EI values were used. These differences disappeared when subcutaneous fat thickness-corrected EI values were considered, allowing for the creation of generic prediction equations (r = 0.41–0.68, p < 0.001). These equations can be used to quantify IMF and EMCL within lower limb muscles from corrected-EI values in non-obese subjects, regardless of the ultrasound device used.