A study aimed to estimate the energy inputs of selected agroforestry systems (AFSs) within the Community-Based Forest Management (CBFM) in Zamboanga City, Philippines was conducted. All Mcal units were converted into Liter Diesel Oil Equivalent (LDOE), where 1.0 LDOE = 11.414 Mcal. Purposive sampling was used in determining the fitted characteristics and the number of respondents required across the 16 CBFM sites, where nine (9) dominant AFSs were identified. A total of 100 respondents were interviewed using a structured questionnaire. The relationships of predictors such as the direct, indirect and embedded energy inputs per AFS were analyzed using descriptive statistics. Means, percentages and sums were compared. The rubber+1based AFS obtained the lowest total energy inputs (TEI) at 5,790.5 Mcal ha<sup>-1</sup> or equal to 507.3 LDOE ha<sup>-1</sup>, while the rubber+3based AFS obtained the highest TEI at 11,801.3 Mcal ha<sup>-1</sup> (1,034.0 LDOE ha<sup>-1</sup>) compared to other AFSs such as the coconut+1based, mango-based, marang-based, lanzones-based, coconut+3based, rubber+2based and coconut+2based with individual TEI that ranged from 6,267.16-11,250.2 Mcal ha<sup>-1</sup> (549.1-985.6 LDOE ha<sup>-1</sup>). Of the total TEI across the nine (9) AFSs, the direct energy input (DEI) contributed 1.6-5.4%, indirect energy input (IEI) 94.1-98.0% and embedded energy input (EEI) 0.3-0.5%, respectively. The TEI is the sum total of DEI, IEI and EEI where each was accounted from pre-land preparation (PLP), crop establishment (CE), crop care and maintenance (CCM), harvest and postharvest (HPH) activities. The high imputed cost on IEI was attributed to high usage of agrochemicals and labor which are identified as the ‘energy hotspots’ or the energy-intensive inputs. The high plant density and number of trees present within the system contributed significantly in the overall TEI. Understanding the significant contributions of various energy-intensive systems will guide policy makers and local planners to initiate an integrated farming approach with reduced energy inputs that is climate smart with higher economic potential for the upland environment in the City of Zamboanga.