The present work provides new insight into the effects of pristine and functionalized carbon nanotubes (CNT's) on the mechanical properties of metakaolin-based geopolymer nanocomposites. Single pristine CNT's and doped CNT-oxide are added to the geopolymer paste at concentrations varying from 0 to 8.31 wt% and from 0 to 10 %, respectively. Reactive molecular dynamics calculations reveal that the mechanical properties of oxide carbon nanotubes deteriorate since covalent bonds created through C-OH interaction lead to defects creation converting their surface SP2 hybridation to SP3. However, they make the structure denser and improve the mobility of CNT's into the matrix. Results show that the diffusion coefficient of CNT-oxide in geopolymer matrix is three times the one of pristine CNT. The tensile tests reveal that the incorporation of a low content of 1.08 wt% pristine CNT increases the elastic and the indentation modulus up to 74% and 94%, respectively. However, for higher concentration, both properties drop with increasing CNT concentration. The addition of 10% doped CNT-oxide leads to a raise of elastic modulus and bulk density by 165% and 22.5%, respectively.