Nearly half of the world's population depends on biomass fuels to meet domestic energy needs, producing high levels of pollutants responsible for substantial morbidity and mortality. We compare carbon monoxide (CO) and particulate matter (PM2.5) exposures and kitchen concentrations in households with study-promoted intervention (OPTIMA-improved stoves and control stoves) in San Marcos Province, Cajamarca Region, Peru. We determined 48-h indoor air concentration levels of CO and PM2.5 in 93 kitchen environments and personal exposure, after OPTIMA-improved stoves had been installed for an average of 7 months. PM2.5 and CO measurements did not differ significantly between OPTIMA-improved stoves and control stoves. Although not statistically significant, a post hoc stratification of OPTIMA-improved stoves by level of performance revealed mean PM2.5 and CO levels of fully functional OPTIMA-improved stoves were 28% lower (n = 20, PM2.5, 136 μg/m3 95% CI 54–217) and 45% lower (n = 25, CO, 3.2 ppm, 95% CI 1.5–4.9) in the kitchen environment compared with the control stoves (n = 34, PM2.5, 189 μg/m3, 95% CI 116–261; n = 44, CO, 5.8 ppm, 95% CI 3.3–8.2). Likewise, although not statistically significant, personal exposures for OPTIMA-improved stoves were 43% and 17% lower for PM2.5 (n = 23) and CO (n = 25), respectively. Stove maintenance and functionality level are factors worthy of consideration for future evaluations of stove interventions.