Rice is the major staple crop worldwide, whereas fertilization practices include mainly the application of synthetic fertilizers. A novel compost was developed using 74% of rice industrial by-products (rice bran and husks) and tested in rice cultivation in Greece’s main rice producing area. Field experimentation was conducted in two consecutive growing seasons (2017 and 2018) and comprised six fertilization treatments, including four compost rates (C1: 80, C2: 160, C3: 320 kg ha−1 of nitrogen all in split application, C4: 160 kg ha−1 of nitrogen in single application), a conventional treatment, as well as an untreated control. A total of 21 morpho-physiological and quality traits were evaluated during the experimentation. The results indicated that rice plants in all compost treatments had greater height (8%–64%) and biomass (32%–113%) compared to the untreated control. In most cases, chlorophyll content index (CCI) and quantum yield (QY) were similar or higher in C3 compared to the conventional treatment. C2 and C3 exhibited similar or greater yields, 7.5–8.7 Mg ha−1 in 2017 and 6.3–6.9 Mg ha−1 in 2018, whereas the conventional treatment resulted in 7.3 Mg ha−1 and 6.8 Mg ha−1 in the two years, respectively. No differences were observed in most quality traits that affect the rice commodity. The current study reveals that in sustainable farming systems based on circular economy, such as organic ones, the application of the proposed compost at the rate of 6 Mg ha−1 can be considered sufficient for the rice crop nutrient requirements.