Under the changing climate, fertilization regimes and weed infestation management in aromatic direct-seeded fine rice (DSR) remain vital for curbing environmental hazards and ensuring food security. A multi-year field study was undertaken to appraise the influence of fertilization techniques and weed-free periods on weed dynamics, nutrient uptake and paddy yield in a semi-arid environment. Treatments included two fertilization methods (broadcasting and side placement) and five weed-free durations (20, 30, 40, 50 post-seeding days, DAS) along with a weed-free crop for a whole season. Weed competition for a season-long crop (weedy check) was maintained for each fertilizer application method. Our results revealed that the side placement of fertilizers resulted in a significantly lower weed density and biomass, even under season-long weed competition. The highest paddy yield was recorded for a crop without weeds, while weed-free duration of up to 50 DAS followed it. The uptake of nitrogen (N), phosphorus (P) and potassium (K) for a weed-free duration of up to 50 DAS were only 19%, 9% and 8%, respectively, as compared to the weedy check. The uptake of N, P and K by weeds in the broadcast method was 18%, 30% and 24% higher, compared to side-placed fertilizers. The period of 20–50 DAS remained critical in DSR as far as weed control was concerned. Thus, the side placement of fertilizers and controlling weeds for up to 50 days after rice sowing can be recommended for general adoption in semi-arid agro-ecological conditions.