The impact of heavy fuel oil (HFO) on the chemical and isotopic composition of submicron particulate matter (PM1) was investigated. For this purpose, we conducted an analysis of water-soluble inorganic ions (WSIIs) and multiple isotopes (δ34S, δ13C, 14C) of PM1 and SO2 collected during two heating periods: before (2021–2022) and during the use of HFO (2022–2023) in Vilnius, Lithuania. The results showed that the combustion of HFO increased the concentrations of SO₂ (by 94%) and PM1-related sulfate (by 30%). It also altered the chemical composition of PM1, with sulfate becoming the predominant component (~40%) of WSIIs. The stable sulfur isotope ratios of SO2 (δ34SSO2) and sulfate (δ34SPM1) shifted significantly to more negative values (δ34SSO2 = 0.4‰, δ34SPM1 = −0.3‰) compared to the previous heating period. Anticorrelation between δ¹³C and δ³⁴S values indicated increased contributions of ¹³C-enriched fossil fuel sources (coal and HFO) in EC, although the share of fossil fuels in elemental carbon (EC) slightly decreased during the HFO period. The combustion of HFO affected the concentrations of PM1 chemical components and substantially impacted the isotopic composition and source contributions of sulfate and EC.