Microplastic (MP) pollution poses an escalating global concern, particularly in the Philippines, which generates over 61,000 metric tons of solid waste daily. This study presents a sustainable and cost-effective method for detecting high-density (HDPE) and low-density polyethylene (LDPE) microplastics using nitrogen-doped carbon dots (N-CDs) synthesized from onion peel and L-cysteine via hydrothermal carbonization. Two precursor ratios (1:1 and 1:0.30 w/w) were evaluated. The resulting N-CDs exhibited bright yellow-green fluorescence (470–500 nm) and excitation-dependent photoluminescence under 365 nm UV light. FTIR and UV-Vis spectroscopy confirmed the presence of nitrogen-containing functional groups and effective graphitization, particularly in the 1:0.30 ratio. Fluorescence imaging revealed stronger intensity and greater stain uniformity in thermally softened MPs treated with 1:0.30 N-CDs, with a peak emission of 10,230.02 a.u. at 2 hours and PMT 11—surpassing the 1:1 ratio. Bandgap and absorbance analyses supported the superior optical behavior of the lower-concentration formulation. Image analysis further indicated increased luminescent area over time, and two-way ANOVA confirmed statistically significant effects of heating time and PMT settings (p < 0.05). Compared to traditional filtration staining, thermal-assisted application offered enhanced and stable fluorescence. These findings demonstrate the efficacy of green-synthesized N-CDs for MP detection, with potential scalability and environmental applicability. Future work should explore alternative biomass sources and assess N-CD performance under field conditions to optimize environmental sensing strategies.