The incidence of duckweed (Lemna minor L.) outbreaks in paddy fields has increased in recent years, but how it impacts rice production is still under debate. This study assessed duckweed’s effects on rice yield and quality under different fertilizer regimes: organic fertilizer (OF), chemical fertilizer (CF), a mix (one-third OF and two-thirds CF based on nitrogen content, COF), and no fertilizer (NF) as a control. For each fertilizer regime, two duckweed treatments were applied: duckweed coverage (Duckweed) and no duckweed coverage (Control). A light wet–dry alternate irrigation method was used in the experimental field. Averaged across all fertilizer treatments, duckweed coverage in paddy fields increased grain yield by 8.3%, mainly due to increased panicle density. Duckweed coverage increased chalky grain percentage by 17.0% under NF, but decreased it by 33.7% under CF, with nonsignificant changes under COF and OF conditions. Similar fertilizer-by-duckweed interactions were also found for chalkiness degree, white degree, breakdown and setback values of the starch rapid visco analyzer (RVA) profile, palatability index, and protein and amino acid concentrations. Duckweed coverage decreased protein and amino acid concentrations but improved the taste of cooked rice under NF, while the opposite trend was observed under CF. Duckweed coverage significantly decreased copper and zinc concentrations in milled rice, which may aggravate the “hidden hunger” risk for rice consumers.