Attenuating the expression of fungal camptothecin biosynthetic genes with subculturing is the challenge that halts their further implementation. The camptothecin productivity of the subcultured Aspergillus terreus has been restored upon addition of Ficus elastica indigenous microbiome; however, the identity of triggering signals of A. terreus camptothecin biosynthesis remains ambiguous. In this study, differential proteomics and metabolomics analyses were implemented to unravel the differentially abundant proteins and metabolites associated with the weakening/restoration of the biosynthetic machinery of camptothecin by A. terreus. The functional proteins, namely, ribosomal proteins, ATP, metal ion, and GTP binding proteins, were abolished by the seventh culture of A. terreus; however, the expression of these proteins was completely restored upon addition of F. elastica microbiome. Among the proteins of highly altered abundance, Pleckstrin homology (PH) domain-containing protein, peptidylprolyl cis/trans isomerase, 60S ribosomal protein, and So-Cu domain-containing proteins were significantly decreased with subculturing of A. terreus and strikingly restored upon addition of F. elastica microbiome. The metabolites 5,7-dihydroxy-2-(4-hydroxyphenyl)-3,6-dimethoxy-4H-chromen and glutaric acid of A. terreus were significantly decreased with subculturing and completely restored upon addition of F. elastica microbiome. The most differentially abundant metabolites were involved in glycolysis, TCA cycle, mevalonate pathway, terpenoids and shikimate synthesis, and ultimately with camptothecin biosynthesis. Thus, overexpression of PH domain-containing protein and peptidylprolyl cis/trans isomerase could be a new avenue for a metabolically stable camptothecin producing A. terreus.