The granulometric fractions of indoor dust, categorized as coarse (grain size of 1.00–0.071 mm) and fine (grain size <0.071 mm), were investigated to discern variations in their magnetic properties and contents of potentially toxic heavy metals. Monthly dust samples were gathered from January 2021 to December 2022 from a private apartment situated on the outskirts of a large urban agglomeration (Warsaw, Poland). To assess indoor dust, several magnetic parameters, including mass-specific magnetic susceptibility, were employed. Portable X-ray fluorescence measurements were utilized to evaluate the enrichment of granulometric fractions in harmful heavy metals. The study reveals a comparable composition of magnetic minerals irrespective of grain size (magnetite and metallic iron), with variations observed in the domain state of magnetic particles (contribution of single-domain (SD) grains to multi-domain (MD)). Seasonal fluctuations were predominantly noted in the distribution of the fine fraction's mass during the warm season (May–July). A notable increase was observed in the fine fraction's mass contribution to the total dust mass compared to the winter season (December and February). The fine fraction was highly enriched in toxic metals, including Pb, Cr, Cu, Mn, Fe, and Sr. Pollution Load index is 6–8 for the fine fraction and 2–8 for the coarse fraction. The increase in the fine fraction mass induces linear changes in magnetic susceptibility, likely associated with the rise in anthropogenic magnetic particles. This finding holds significant implications for human health, as fine particles laden with toxic heavy metals can enter the human respiratory tract causing adverse health effects.