Seaweed extract is known to contain nutrients and growth-regulating substances that affect soil biota, and a source of protection against pests and diseases. Earthworm, which is an example of a soil biota and playing the role of ecosystem engineer, has the ability to produce suitable land biostructures, for the inhabitation of arbuscular mycorrhizal fungi (AMF), which has an impact on upland rice growth. Therefore, this study aims to determine, (i) the effect of seaweed extract on the population of earthworms and spores of arbuscular mycorrhizal fungi, and (ii) the impact of the engineered soil on the growth of local upland rice varieties. Furthermore, the extract of seaweed, such as Kappapychus alvarezii, was divided into five concentration levels, namely 0%, 20%, 40%, 60%, and 80%. Each treatment was drenched into the soil from the cogongrass vegetated area, mixed with 20 Pheretima sp., and maintained for 49 days in the greenhouse. The result showed that the total difference in the earthworms’ concentration treatments was not significant. It also showed that the total AMF spores in the engineered soil products of 20% concentration was the highest. Based on treatment with the earthworm engineered soil products, the highest and lowest vegetative growth and yield components of upland rice were observed at the concentrations of 80% and 0%, respectively. In conclusion, the application of seaweed extract to the soil did not significantly reduce the earthworm population. The extract concentration of 20% also increased the total AMF spore in the engineered soil. Moreover, highly treated engineered soil products increased the growth and yield components of upland Kambowa rice on cogongrass soils.