Deep energy retrofits (DER) for residential housing have been proposed to reduce greenhouse gas emissions; these result in ~50% additional energy efficiency compared to standard renovations, energy star (ES) renovations. However, the impact of increased energy efficiency on indoor air quality (IAQ) is poorly understood. We conducted a longitudinal study to compare IAQ and occupant comfort in 12 low income single-family homes renovated to a DER or ES standard. Quarterly visits were conducted for a median of 18 months post-renovation; IAQ was assessed in 4 rooms per visit for a total of 237 measurements. Multivariable regression models accounted for repeated measurements and controlled for house-and family-related covariates. In fully adjusted models, average difference (95% confidence interval) in IAQ parameters in DER homes versus ES homes were: temperature: -0.3 C (-1.2, 0.6); relative humidity: 0.4 % (-1.1, 1.8); carbon dioxide: 43.7 ppm (-18.8, 106.2); and total volatile organic compounds: 198 ppb (-224, 620). Residents in DER homes were significantly less likely to report their homes were comfortable, most likely due to initial difficulties with new heating system technology. We found no differences in IAQ between DER and ES homes; however, education is strongly recommended when incorporating new technology into residences.