Coffea canephora, also known as Robusta, is one of the coffee species that dominates production in Indonesia. The morphology, physiology, and phytochemistry of Canephora coffee beans are affected by many factors, such as the fruit harvesting time and post-harvest processing. The maturity stage of coffee fruits at harvest time and post-harvest management will affect the various morpho-physiological and phytochemical compositions of the coffee beans. This research aimed to observe Canephora coffee beans’ morpho-physiological and phytochemical compositions for various harvesting stages and soaking durations. The experiment was conducted using a completely randomized design (CRD). It tested eight treatments, a combination of harvesting times (H1 = only red fruit/ripe stage, H2 = green, yellow, red fruits/strip-picking stage) and soaking durations (S0 = 0, S1 = 12, S2 = 24, and S3 = 36 h) with four replications. The main observations were the morpho-physiological traits (size, weight, color, moisture content, bean yield) and the phytochemical compositions (TPC = total phenolic content, AA = antioxidant activity, and CC = caffeine content) of the coffee bean before and after the drying process. Based on morphological characteristics (bean size and weight before drying), the highest value came from selective harvesting or ripe-picking only without soaking duration application (H1S0). While the selective harvesting method with a 24 h soaking duration showed a high value for the color trait (L and b*), the treatment that affected the color trait after drying was the strip-picking harvesting method without soaking (a* and b*). On the other hand, the phytochemical contents had H1S0 for the highest TPC and AA values. In contrast, H1S1 or selective harvesting, with 12 h of soaking, had the highest value of CC. The optimum combination of harvesting methods and soaking duration will improve the quality of the Canephora coffee beans.