Men who have sex with men (MSM) reporting higher HIV risk behavior over time are often more adherent to pre-exposure prophylaxis (PrEP), but it is unclear if recent risk behavior and partnership type affect long-term PrEP adherence. HIV-negative MSM and transgender women completing the 48-week randomized study TAPIR (Daily Text Messages to Support Adherence to PrEP in At-Risk for HIV Individuals) were included. At baseline and weeks 24 and 48, a modified Calculated Risk (mCalcR) Score estimated the likelihood of HIV seroconversion over 1 year based on reported condomless anal sex acts in the last month and current sexually transmitted infection. mCalcR scores were categorized as low, moderate, and high/very high risk. Partnership type was classified as no partner/single HIV-negative partner (no/single−), single HIV-positive partner (single+), or multiple partners of any serostatus (multi) in the past 3 months. PrEP adherence was measured by intracellular tenofovir-diphosphate (TFV-DP) levels. Among 313 individuals, there was no difference in mCalcR category from baseline to week 48. There was a significant change in partnership type, with no/single partnerships increasing from 0.5% to 9%. Participants with moderate and high/very risk had higher TFV-DP levels than the low-risk group. No/single participants had lower TFV-DP levels than those reporting single+ or multi. Although there was a shift toward lower-risk partnerships, HIV risk category remained stable over time. Individuals with riskier behaviors and partnerships had higher PrEP drug levels, suggesting continued motivation for and adherence to PrEP.