A typical case of multiple-use forest management (MFM) in Southwestern Amazon is the commercial harvesting of Amazon or Brazil nut (Bertholletia excelsa) seeds and of timber of other tree species. Although the Amazon nut is the most important non-timber forest product (NTFP) in the Amazon basin, the species is under serious threat due to deforestation and may also be affected by overharvesting. However, selective logging of other tree species coexisting with Bertholletia may positively affect Bertholletia populations, thus enabling a special case for MFM. For this research, we investigated the impact of the intensity of Amazon nut harvesting and timber logging on Bertholletia populations in the Bolivian Amazon. We used demographic data from 72 two-hectare transects located within 24 community-based household forests varying in the intensity of nut collection (0–100%) and timber logging (0–15% of logging-disturbed forest area). Simulated Bertholletia population size increased with logging intensity but decreased with Amazon nut harvesting intensity. Bertholletia populations were projected to grow at the average MFM harvesting scenario tested: 57.4% of nut harvesting, 5.3% of logging-disturbed area (λ100 = 1.011). Our simulations also revealed that up to 89% of Amazon nut seeds can be harvested while sustaining Bertholletia populations, under 15% of logging-disturbed area, and applying liana cutting. Modest levels of timber logging and application of liana cutting may compensate for the negative effect of Amazon nut collection on Bertholletia populations for the next century. Our study demonstrates that Amazon nut and timber production could be combined in a sustainable MFM scheme, thus increasing the economic value of managed tropical forests and its promotion to reduce the increasing pressure by deforestation.