A study was under taken to isolate and screen selected beneficial microbes, which can restore soil fertility in the chosen flood-affected areas of Attapady and Nelliyampathy in Palakkad district of Kerala, India. A total of 76 isolates (40 N-fixers, 26 P-solubilizers and 10 K-solubilizers) were obtained from the flood affected areas. Triple enzyme activities of cellulase, laccase and dehydrogenase were recorded in 47.36% of N-fixers from Attapadi, 36.36% P-solubilizers and 60% K-solubilizers from Nelliyampathy. Six diverse maximal enzyme producers were selected based on study of microbial dry weight and plant growth-promoting characteristics, including nitrogen(N) fixation, phoshphate(P), potassium(K), and indole acetic acid(IAA) synthesis. These 6 isolates were ranked according to all the evaluated characteristics using statistical analysis, and the top 3 isolates were found. The most efficient multi-functional N-fixer was identified as Priestia megaterium from Attapadi which ranked first, Aspergillus terreus as the most capable P-solubilizer from Nelliyampathy and Talaromyces pinophilus as the most proficient K-solubilizer from Nelliyampathy. The competence of these three isolates from flood affected regions could help in the rejuvenation of the soil organic matter (SOM) in degraded soils. However further evaluation under field conditions are required to confirm these results.